Index (mitobo 2.0 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

a - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Implicit curve parameter a.
A - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Optimization matrix A, to be modified by snake energies in each iteration.
Abl_X(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Calculate the x-derivative of the gradient image.
Abl_Y(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Calculate the y-derivative of the gradient image.
abs(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Absolute values of the image elements.
abs(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Absolute values of the image elements.
abs_diff(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Absolute difference of the elements of two images
absDiff(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Absolute difference of two images.
AbsenceDetectionMethod() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.AbsenceDetectionMethod
AbstractAssociationDistribution<S extends Copyable<?>,T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts: Abstract class for association distributions that allow sampling of the association variables for a set of observations in a multi-target tracking framework.
AbstractAssociationDistribution(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, DataAssociationFactory) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution: Constructor
AbstractMultiObservationDistribution<S extends Copyable<?>,T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts: Abstract class for multi target observation distributions.
AbstractMultiObservationDistribution(AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<S>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution: Constructor to set the condition conditionX, and the factories of multi state and multi observation variables
AbstractMultiObservationDistributionIndep<S extends Copyable<?>,T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts: Abstract class for multi target observation distributions.
AbstractMultiObservationDistributionIndep(AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<S>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep: Constructor to set the condition conditionX, and the factories of multi state and multi observation variables
AbstractMultiState<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts: Abstract class to hold the states of multiple targets.
AbstractMultiState(AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState: Constructor that assigns a factory
AbstractMultiStateFactory<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts: Factory class for creating new multi state objects
AbstractMultiStateFactory(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory: Constructor with specification of the variables of a single state
AbstractMultiStateTransitionDistribution<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts: Abstract class for multi-target state transition distributions.
AbstractMultiStateTransitionDistribution(AbstractMultiState<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution: Constructor to set the condition X, and the factories of multi state and multi observation variables
AbstractMultiStateTransitionDistributionIndep<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts: Abstract class of multi-target state transition distribution with independent targets.
AbstractMultiStateTransitionDistributionIndep(AbstractMultiState<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistributionIndep
accept(File) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components.MTBTableWindow.DataTabFileFilter
accept(File) - Method in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
acceptStacks(File) - Method in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
accuracy - Static variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Local accuracy for comparisons of values against zero.
acot(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Return the arcus cotangens of value in radian.
ActinAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton: Operator for analyzing actin filament structures in 2D images.
ActinAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Default constructor.
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowButton
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel: Fires a PropertyChangeEvent with property CheckBoxPanel.CHECK_CHANGED_PROPERTY if a checkbox value was changed
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane: Assigns the reader options to the option variables when a file selection is approved by the file chooser.
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane: Assigns the writer options to the option variables when a file selection is approved by the file chooser.
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel: Assigns the selected radio button string and fires a PropertyChangeEvent with property RadioButtonPanel.SELECTION_CHANGED_PROPERTY
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
activeImage - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Image currently under processing.
activePlus - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Reference to currently active image.
activeProcessor - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Reference to processor of currently active image LabelImageEditor.activePlus.
activeSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Array with active snakes.
activityArray - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult: Vector tagging regions as active or not during presegmentation phase.
activityArray - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Array of active snakes, suitable for masking snakes in optimization.
actualSliceOnly - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
adaptedGamma - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate: The new and adapted gamma values for all snake points.
adapter - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator: Adapter object to be iterated over.
adaptGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed: Gamma adaptation using fixed decreasing factor for all gamma values.
adaptGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone: No gamma adaptation is made.
adaptGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner: Gamma adaptation using a point wise adaptation, depending on the current snake and the external energy force.
adaptGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate: Method for gamma adaptation.
add(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
add(MTBBorder2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Append a border (at the end) to the set of borders.
add(MTBContour2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Append a contour (at the end) to the set of contours.
add(MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: add histogram data to this MTBHistogram object.
add(MTBLineSegment2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: Append a new segment (at the end) to the set of line segments.
add(Point2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
add(MTBPolygon2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Append a polygon (at the end) to the set of polygons.
add(MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Append a region (at the end) to the set of regions.
add(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag: Add a region set to this bag
add(MTBRegion3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Append a region (at the end) to the set of regions.
add(MTBSurface3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Append a region (at the end) to the set of regions
add(MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Appends the specified element to the end of this list.
add(MTBNeurite2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet: Appends the specified element to the end of this list.
add(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Method to add two images.
add(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Add a constant to each image value
add(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Add the elements of two images
add(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Add a constant to each image value
add(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Add the elements two images
add(TrackEvaluator.TrackEvaluatorResult) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
addActionListenerToButtons(ActionListener) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: Adds external action listeners to buttons.
addAll(MTBPoint2DSet) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
addBordersToRoiManager(MTBBorder2DSet) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Adds a set of 2D borders to the ROI manager.
addChild(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: Add a new child to the node.
addCloseButtonPanel() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Adds set of control buttons to the main panel.
addContoursToRoiManager(MTBContour2DSet) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Adds a set of 2D contours to the ROI manager.
addCurrentInfo(double, DataAssociation, AbstractMultiState<T>, Set<Short>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: Add sample info of the current time step
addData(Vector<Vector<Point2D.Double>>, Vector<Vector<Line2D.Double>>, int[], Vector<Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Add data to the current neurite object.
addEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Add a edge to MTBGraph.
addElementAt(int, MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Inserts the specified element at the specified position in this list.
addElementAt(int, MTBNeurite2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet: Inserts the specified element at the specified position in this list.
addEnergy(T, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: Append another energy to the list.
addEnergy(T) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: Append another energy to the list with default weight 1.0.
addEnergy(MTBLevelsetEnergyDerivable, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Append another energy to the list.
addEnergy(MTBLevelsetEnergyDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Append another energy to the list with default weight 1.0.
addEnergy(MTBSnakeEnergyComputable, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable: Append another energy to the list.
addEnergy(MTBSnakeEnergyComputable) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable: Append another energy to the list with default weight 1.0.
addEnergy(MTBSnakeEnergyDerivable, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable: Append another energy to the list.
addEnergy(MTBSnakeEnergyDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable: Append another energy to the list with default weight 1.0.
addEnergyButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Add button for energies.
addFeatures(double, double[]) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer: add the given patterns (feature arrays) together with their corresponding label to the existing patterns used to train the SVM
addFile(String) - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData: Adds a file to the list of the node.
addFirst(MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Inserts the specified element at the beginning of this list.
addImage(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
addIndentationSegments(LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment>) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Add list of indentation segments to object.
addIndepGaussian(GaussianDistribution, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians: Add an independent Gaussian state distribution
addInEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Add a incoming MTBGraphEdge to the MTBGraphNode
addInflectionPoints(LinkedList<MorphologyAnalyzer2DInProData.InflectionPoint>) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Add list of inflection points to object.
addInner(MTBBorder2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Add an inner border to the existing border object.
addInner(MTBBorder2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Add a inner contour to the existing contour object.
addInnerContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Adding the possible inner contours to the outer contour of a region.
additionalResultsWanted - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Flag to activate calculation of additional result images.
addLast(MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Appends the specified element to the end of this list.
addMarker(CellCntrMarker) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Adds a marker to the vector.
addNewResult(SegResult_Complete) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel
addNode(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Add a node to MTBGraph.
addOutEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Add a outgoing MTBGraphEdge to the MTBGraphNode
addParameterInputFields(JPanel) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Adds the input fields for all relevant parameters.
addPixel(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Add a 2D point to the existing border.
addPixel(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Append a point to the region from the given coordinates.
addPixel(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Append a point to the region from the given point object.
addPoint(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
addPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Appends a new point to the end of the polygon.
addPoint(MTBPoint3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Append a 3D point to the region.
addPoint(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Append a point to the region from the given coordinates.
addPoint(MTBPoint3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D: Append a 3D point to the region.
addPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Overwrites Polygon2D method.
addPolygonsToRoiManager(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Adds a set of polygons to the ROI manager.
addPolygonToRoiManager(MTBPolygon2D) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Adds the given polygon to the ROI manager.
addProtrusionSegments(LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment>) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Add list of protrusion segments to object.
addRegionsToRoiManager(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Adds a set of 2D regions to the ROI manager.
addResult(FeatureCalculatorResult[]) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult: Adds result data to the object.
addResultImages - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Vector of additional result images.
addResultImages(FeatureCalculatorResult[]) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Generates a visual representation of the tile data and stores it.
addSegmentationResult(SegResult_Particles) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Method is to be called for cleaning-up the operator resources.
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
addSubgraph(MTBGraph, Color) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter: Specify a subgraph that is to be painted in the given color.
addSubgraphAdjaceny(AdjacencyMatrix<T>, Color) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter: Specify a subgraph that is to be painted in the given color.
AdjacencyMatrix<T extends Comparable<?>> - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces: Interface for the adjacency matrix of a graph.
adjmatrix - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
adjMatrix - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
adoptSliceLabels(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Copy slice labels from src to this
algorithm - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: The algorithm used for estimating the curvature.
Algorithm() - Constructor for enum de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator.Algorithm
alpha - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
alpha - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Weighting factor for snake length term.
alphaDecrease - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix: Value by which alpha is decreased in each iteration.
alphaInitial - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Initial weighting factor for the length term, should be > 0.
alphas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Vector of point-specific alpha values.
alphaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt: Update function for alpha values.
alphaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
alphaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone: Update function for alphas.
analysisDisplayImg - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Image illustrating analysis results.
analyzedImages - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Vector with all analyzed image files.
analyzeIntensities - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
analyzeIntensities - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
analyzeIntensities(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
analyzeLocalCurvatures() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Calculates and analyses pixel-wise local curvatures.
analyzeProtrusionsIndentations - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Flag to turn on/off analysis of protrusions and indentations.
analyzerList - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult: Set of feature calculator identifiers.
analyzeShapes - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
analyzeShapes - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
analyzeShapes(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
analyzeTrajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
analyzeTrajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
analyzeTrajectories(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
and(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Bitwise logical AND of two images.
and(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Bitwise logical AND of two images.
angle(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
angle - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D: Orientation of the filter.
angleDiff360(double, double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
angleDiff360(double, double) - Static method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Compute angle difference of two angles in interval 0 up to 360 degree
angleDiffPM180(double, double) - Static method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Compute angle difference of two angles in interval -180 up to 180 degree
angleSampling - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Angular sampling step size.
angleSampling - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Angular sampling interval.
angleSampling - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D: Sampling step size for orientations.
angleSampling - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Sampling step size for orientations considered.
angularSecondMoment - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
apicalLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Apical length of the segment, from equator to top.
ApplicationMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D.ApplicationMode
applyComponentWise - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Flag to activate component-wise application, yields a binary result image.
applyMask(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate: Invokes dilation.
applyMask(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode: Invokes erosion.
applyMaskBinary(MTBImage, int, int, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate: Applies a dilation mask to the given binary image.
applyMaskBinary(MTBImage, int, int, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode: Applies an erosion mask to the given binary image.
applyMaskGray(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate: Applies a dilation mask to the given intensity image.
applyMaskGray(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode: Applies an erosion mask to the given intensity image.
applyNiblackThreshold(MTBImage, int, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: This function implements the conventional (enhanced) Niblack binarization.
applyNiblackThreshold_withLocalVarCheck(MTBImage, int, double, double, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: This function implements the conventional Niblack binarization, enhanced with a local variance check.
applyNiblackThresholdMaskwise(MTBImage, int, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Enhanced Niblack binarization applied maskwise to the image, i.e. all pixels inside the mask get the same threshold.
applyNiblackThresholdWholeImage(ImageProcessor, double, double, ImagePlus) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Deprecated.
applyNiblackThresholdWholeImage(MTBImage, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: This function implements the conventional (enhanced) Niblack binarization.
applyRamerDouglasPeuckerAlgorithm(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet: Algorithm idea: - Urs Ramer, "An iterative procedure for the polygonal approximation of plane curves", Computer Graphics and Image Processing, 1(3), 244–256 (1972) doi:10.1016/S0146-664X(72)80017-0 - David Douglas & Thomas Peucker, "Algorithms for the reduction of the number of points required to represent a digitized line or its caricature", The Canadian Cartographer 10(2), 112–122 (1973) doi:10.3138/FM57-6770-U75U-7727 Implementation according to: https://www.namekdev.net/2014/06/iterative-version-of-ramer-douglas-peucker-line-simplification-algorithm/
applyRamerDouglasPeuckerAlgorithm(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet: Calls MTBPoint2DSet.applyRamerDouglasPeuckerAlgorithm(int, int, double) with the first and last point of the point list.
applyVesselnessFilter(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Gaussian smoothing and vesselness enhancement filtering.
approxFunction - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives: Helper to calculate values of approximated Dirac impulse function.
ApproxVersion() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper.ApproxVersion
area - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Size of region in pixels.
areaFraction - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff: Area fraction factor.
areaFraction - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset: Area fraction factor.
ArealParameterExtractor - Class in de.unihalle.informatik.MiToBo.apps.biofilms: operator for calculating areal parameters from biofilm images as described in Yang et al., Quantifying biofilm structure using image analysis.
ArealParameterExtractor() - Constructor for class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
ArealParameterExtractor(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
arealPorosity - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
areas - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
areas - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
areas - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Region sizes, entry with index 0 is assumed to refer to background.
areas - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Region sizes.
areas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
areAssociated(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive: Determine if target and observation are associated.
areAssociated(int, int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation: Ask if the specified target and observation are associated
areRegionsInManagerAvailable() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Returns true if there are regions available in ROI manager.
arithmeticOp - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
ArithOp() - Constructor for enum de.unihalle.informatik.MiToBo.math.images.ImageArithmetics.ArithOp
ArrayFilterDouble1D - Class in de.unihalle.informatik.MiToBo.math.arrays.filter: This class defines a superclass for filters for 1D arrays.
ArrayFilterDouble1D() - Constructor for class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D: Default constructor.
ArrayToColorMapImage - Class in de.unihalle.informatik.MiToBo.visualization.colormappings: This operator visualizes a 2D array using a specified color mapping.
ArrayToColorMapImage() - Constructor for class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: Default constructor.
ArrayToColorMapImage(double[][]) - Constructor for class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: Constructor.
ArrayToColorMapImage.RangeColor - Enum in de.unihalle.informatik.MiToBo.visualization.colormappings: Possible colors to colorize value ranges.
assign(MTBRegion2DSet, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite: assign regions from one frame to regions from another frame
assignStructsToCell_com(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Assigns the given set of structure regions to individual cells.
assignStructsToCell_overlap(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Assigns the given set of structure regions to individual cells.
assocDistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
assocfactory - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution: factory for the data association object
AssociationDistribution<S extends TargetID,T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl: Association distribution to sample association variables for a set of observations based on a model of how observations are formed.
AssociationDistribution(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, LogProbabilityMassFunction, LogProbabilityMassFunction, double) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Constructor.
AssociationDistribution(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, LogProbabilityMassFunction, LogProbabilityMassFunction, double, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Constructor where the maximum number of observations in the time series is specified to avoid some re-computations.
AssociationDistributionNN<S extends TargetID,T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl: Association distribution to sample association variables for a set of observations based on a model of how observations are formed.
AssociationDistributionNN(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, LogProbabilityMassFunction, LogProbabilityMassFunction, double, int, double) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN: Constructor.
AssociationDistributionNN(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, LogProbabilityMassFunction, LogProbabilityMassFunction, double, int, int, double) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN: Constructor where the maximum number of observations in the time series is specified to avoid some re-computations.
AssociationDistributionNN.AType - Enum in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
AssociationDistributionNN.ObsDistance - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
AssociationDistributionNN.ProbTreeData - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
assocObs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
aTrousDWT(MTBImage, int, MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: A trous DWT
AType() - Constructor for enum de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.AType
auto - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
availableClasses - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: List of available energies.
availableCodecs(Class<? extends IFormatWriter>) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils: Get available codecs of a specific writer class.
availableQualities(Class<? extends IFormatWriter>) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils: Get available qualities of a specific writer class.
averageDeltas(double[], int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Return the averaged deltas, i.e.
averageRegionIntensities - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Vector of average region intensities.
avgApicalIndentationLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Average of apical indentations lengths.
avgApicalIndentationLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgApicalProtrusionLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Average of apical protrusion lengths.
avgApicalProtrusionLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgBasalIndentationLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Average of basal indentation lengths.
avgBasalIndentationLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgBasalProtrusionLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Average of basal protrusion lengths.
avgBasalProtrusionLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgBaselineIndentationLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Average length of indentations baselines.
avgBaselineIndentationLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgBaselineProtrusionLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Average length of protrusion baselines.
avgBaselineProtrusionLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgBranchLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgConcavities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgDiffusionDist - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
avgEndpointDistances - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgEquatorIndentationLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Average length of indentation equators.
avgEquatorIndentationLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgEquatorProtrusionLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Average length of protrusion equators.
avgEquatorProtrusionLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgFactor - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
avgHorizontalRunLength - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
avgIndentationLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Average length of indentations.
avgIndentationLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgIntensity - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape: Average intensity of all shape pixels.
avgLobeDepths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgNeckDepths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgNeuriteWidths - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Vector of neurite widths, containing 3 elements. 1. average width of whole neurite, 2. average width of neurite shaft, and 3. average width of growth cone.
avgProtrusionLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Average length of protrusions.
avgProtrusionLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
avgsize_cells - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Average size of cells.
avgsize_nuclei - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Average size of nuclei.
avgsize_particles - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Average size of particles.
avgVerticalRunLength - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
AwtColorDataIOCmdline - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline: Data I/O provider for Cmdline-OpRunner for java.awt.Color objects.
AwtColorDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtColorDataIOCmdline
AwtColorDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Data I/O provider for GUI-OpRunner for java.awt.Color objects.
AwtColorDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
AwtColorDataIOSwing.ColorChooserPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Panel with configuration elements.
AwtColorDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans: Xmlbeans provider for java.awt.Color objects.
AwtColorDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtColorDataIOXmlbeans
AwtPoint2dDataIOCmdline - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline: Data I/O provider for Cmdline-OpRunner for java.awt.geom.Point2D.Double objects.
AwtPoint2dDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtPoint2dDataIOCmdline
AwtPoint2dDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans: Xmlbeans provider for java.awt.Color objects.
AwtPoint2dDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtPoint2dDataIOXmlbeans

B

b - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Implicit curve parameter b.
B - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: External energy vector, to be modified by snake energies.
background_color - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
BACKGROUND_PIXEL - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
backgroundLabel - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
backwardDifferencing_X(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
backwardDifferencing_X(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
backwardDifferencing_Y(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
backwardDifferencing_Y(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
backwardDifferencing_Z(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
backwardDifferencing_Z(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
basalLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Basal length of the segment, from baseline to equator.
baselineConstant - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Baseline constant.
baselineLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Length of segment baseline.
BasicMorphology - Class in de.unihalle.informatik.MiToBo.morphology: class implementing basic morphological operations (for use with grayscale as well as with binary images)
BasicMorphology() - Constructor for class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
BasicMorphology(MTBImage, MTBStructuringElement) - Constructor for class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
BasicMorphology(Integer, BasicMorphology.opMode, BasicMorphology.maskShape) - Constructor for class de.unihalle.informatik.MiToBo.morphology.BasicMorphology: Constructor to create new BasicMorphology object with mask size, mode and shape of the structuring element.
BasicMorphology.maskShape - Enum in de.unihalle.informatik.MiToBo.morphology
BasicMorphology.opMode - Enum in de.unihalle.informatik.MiToBo.morphology
beta - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
beta - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Weighting factor for snake curvature term.
betaDecrease - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix: Value by which beta is decreased in each iteration.
betaInitial - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Weighting factor for the curvature term, should always be > 0.
betas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Vector of point-specific beta values.
betaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt: Update function for beta values.
betaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
betaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone: Update function for betas.
BG_PHASE - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Level set function value to represent the background phase
bg_value - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
bgLabel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
bgLabel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
bgLabel - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
bgLabel - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
bgValue - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
binaryCorrelationImages - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Stack of binarized correlation images.
binaryImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
BinaryImageEndpointTools - Class in de.unihalle.informatik.MiToBo.morphology: Tool functions for extracting endpoints and branches from binary images, particularly images of skeletons.
BinaryImageEndpointTools() - Constructor for class de.unihalle.informatik.MiToBo.morphology.BinaryImageEndpointTools
binaryMasks - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: (Optinal) stack with binary segmentation masks.
binFilteredImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Intermediate result: binarized vesselness image after filtering.
binMask - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Binary segmentation mask.
binMask - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Binary segmentation mask.
binning(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: change the binning of the histogram
binomial(int, int) - Static method in class de.unihalle.informatik.MiToBo.math.MathX: Binomial coefficient of n over k
binVesselImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Intermediate result: binarized vesselness image.
blacklist - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
blackTophat(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology: calculates the black tophat transform, i.e. difference of the closing of the image and the image
(also called closing tophat)
blue - Static variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Definition of blue color.
BLUE_COMPONENT_INDEX - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
BorderBackgroundContrast() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.BorderBackgroundContrast
BorderBackgroundContrast() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D.BorderBackgroundContrast
BorderConnectivity() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D.BorderConnectivity
borderContrast - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Border to background relation.
borderContrast - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Border to background relation.
borderDist - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Safety distance along image borders.
borderSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: The set of borders represented as a Vector.
borderSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI: Set of 2D borders.
borderSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI: Set of borders of the 2D regions.
BordersOnLabeledComponents - Class in de.unihalle.informatik.MiToBo.segmentation.contours.extraction: Class to extract borders from connected components.
BordersOnLabeledComponents() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Standard constructor.
BordersOnLabeledComponents(MTBImage, MTBRegion2DSet, MTBBorder2D.BorderConnectivity, BordersOnLabeledComponents.BorderType, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Constructor.
BordersOnLabeledComponents.BorderType - Enum in de.unihalle.informatik.MiToBo.segmentation.contours.extraction: Possible types of borders to be extracted.
borderType - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Type of borders to be extracted.
BorderType() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents.BorderType
boundaryChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Channel of input image containing stained cell boundaries.
BoundaryPadding() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow.BoundaryPadding
boundaryPadding - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
boundaryPadding - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
boundaryPadding - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
BoundEnsure(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Test the image boundary.
BoundExpand(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Expand the image boundary.
BoundShrink(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Shrink the image boundary.
boxLinksImagePlus - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess: Associative list for links between ImagePlus and associated image boxes.
boxLinksMTBImage - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess: Associative list for links between MTBImages and associated image boxes.
boxWhiskerChart - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Resulting box-whisker chart.
BoxWhiskerChartPlotter - Class in de.unihalle.informatik.MiToBo.visualization.plots: Operator that generates box-whisker plots using JFreeChart.
BoxWhiskerChartPlotter() - Constructor for class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Default constructor.
boxWhiskerCharts - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Box-whisker plot of the group-wise cluster distributions.
boxWhiskerCharts - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Box-whisker plot of the group-wise cluster distributions.
branchCounts - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
bthImage - Variable in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Black top-hat image.
bthMaskSize - Variable in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
build(int, int, MTBImageByte, MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Internal method to create the graph from the skeleton image.
buildMainPanel(Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Build the main panel for configuring the list of energies.
buildMainPanel() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Build the main panel for configuring the list of energies.
buildSkeletonGraph(int, int, int, int, MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Build the skeleton graph from a given binary skeleton image and a given starting point to build up the graph.
button - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
button - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowPanel: Button associated with the panel.
button - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowPanel: Button associated with the panel.
buttonEdit - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel: Button to edit loaded data or insert data manually.
buttonLoad - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel: Button to load data, e.g., from file or ROI manager.
buttonLoad - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel: Button to load data, e.g., from file or ROI manager.
buttonReset - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel: Button to delete currently loaded data.
buttonReset - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel: Button to delete currently loaded data.
buttonShow - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
BWImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
BYTE_TO_DEGREE - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Constants to convert from [0-255] to [0-359] and vice versa.

C

C - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
c - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
c - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Implicit curve parameter c.
C - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Covariance matrix calculated from mean-free data.
c - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE: array to hold means of phases, starting with MTBLevelsetMembership.BG_PHASE
c - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
C2DtoMTB(C2DPolygon) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper: Converts a C2D polygon to the MiToBo polygon data type.
calcAngularSecondMoment(Double[][]) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
calcArea - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
calcArea() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
calcArealPorosity(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
calcASM - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
calcAverageDiffusionDistance(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
calcAverageSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Calculates the average size of the set.
calcAvgDiffusionDistance - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
calcAvgHorizontalRunLength - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
calcAvgHorizontalRunLength(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
calcAvgVerticalRunLength - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
calcAvgVerticalRunLength(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
calcBranchLength(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Calculates the lenght of the given branch.
calcCentre(Vector<MTBPoint3D>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Calculate the centroid (not yet normalized by volume) of a given vector of points.
calcCircularity - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
calcCircularity() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
calcCompactness - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
calcCompactness() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
calcConcavityData - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Flag to turn on/off analysis of concavities.
calcContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Get all inner- and outer-contours for the given regions.
calcConvexHullMeasures - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Flag to turn on/off analysis of convex hull.
calcDilationAreas - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
calcDilationAreas(MTBImage, int, int) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
calcDM() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Method to calculate the distance map of the given binary image using the Chamfer-algorithm.
calcEccentricity - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
calcEccentricity() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
calcEllipseParameters() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Calculate concrete ellipse parameters from implicit equation.
calcEnergy(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Calculates the absolute energy value for the given segmentation.
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Calculates normalized snake energy.
calcEnergy(SnakeOptimizerSingle, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Calculates length term of snake energy at a certain position for the current snake.
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Calculates snake energy (non-normalized!).
calcEnergy(SnakeOptimizerSingle, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Calculates energy at a certain position for the current snake.
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Calculates the current energy of the snake.
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
calcEnergy(SnakeOptimizerSingle, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Calculates energy at a certain snake point.
calcEnergy(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable: Calculates the energy of the current snake.
calcEnhancedImage(MTBImage, double, int, boolean) - Static method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Calculates the new image intensity values of the image.
calcEntropy - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
calcEntropy(MTBImageHistogram) - Static method in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization: Calculates the Shannon entropy for the given (normalized!)
calcFeatureFlagChanged() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Callback routine to change parameters on change of flag for enable/disable feature calculation.
calcFeatureFlagChanged() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Callback routine to change parameters on change of flag for enable/disable feature calculation.
calcFeatures(double[][]) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures: Extracts Haralick features from given matrix.
CalcGlobalThreshOtsu - Class in de.unihalle.informatik.MiToBo.segmentation.thresholds: This class implements Otsu's method for calculating an optimal threshold for a given grayscale images.
CalcGlobalThreshOtsu() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu: Default constructor.
CalcGlobalThreshOtsu(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu: Default constructor with input image as argument.
CalcGlobalThreshOtsu(MTBImageHistogram) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu: Default constructor with input histogram as argument.
CalcGlobalThreshOtsu.InputType - Enum in de.unihalle.informatik.MiToBo.segmentation.thresholds: Type of input to work on.
calcGVF() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Calculate the GVF field with the given number of iterations on the given input image.
calcIDM - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
calcInteriorEnergy(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Calculates the interior part of energy value for the given segmentation.
calcInverseDifferenceMoment(Double[][]) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
calcLengthWidth - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
calcLengthWidth() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
calcMarginRoughness - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Flag to turn on/off calculation of margin roughness.
calcMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite: Function calculating actual matching, to be implemented by subclasses.
calcMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
calcMatching_mainTest() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Checks whether a valid solution has been found.
calcMatching_stageOne() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Implements stage one: searching for new candidate matches.
calcMatching_stageThree() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Implements stage three: decrease scores to generate new zero entries.
calcMatching_stageTwo(int, int) - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Implements stage two: extracting exchange chain.
calcMatrix(FeatureCalculatorHaralickMeasures.HaralickDirection) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures: Extracts the co-occurence matrix for the given distance and direction.
calcMaxDiffusionDistance - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
calcMaximumDiffusionDistance(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
calcMaxSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Calculates the maximum size of the set.
calcMean(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Return the mean value of an array of double.
calcMedian(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Returns the median value of an array of double.
calcMinMax(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Returns the min and max value.
calcMinSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Calculates the minimum size of the set.
calcMode - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
calcNormSpatialDependenceMatrix(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
calcPerimeter - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
calcPerimeter() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
calcPorosity - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
calcPotential_approxLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Calculates an approximation of the potential of the field by gradient descent.
calcPotential_exactLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Calculates the potential of the field by solving a LSE with least squares.
calcPotential_exactLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder: Exact least squares reconstruction of the potential.
calcPotential_gradientDescent(boolean) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder: Reconstruct potential via gradient descent.
calcPotential_incrementalLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder: Reconstructs the potential of the vector field incrementally.
calcPotential_incrLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Calculates a rough approximation of the potential of the field in linear time.
calcPrecision(int, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures: Calculates the precision from given true and false positives.
calcProfile() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
CalcQualityMeasures - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation: Helper class for calculating precision and recall values.
CalcQualityMeasures() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures
CalcQualityMeasures.PrecisionCalc - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation: Internal operator for precision calculation.
CalcQualityMeasures.RecallCalc - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation: Internal operator for recall calculation.
calcRadiusImage - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Flag to enable calculation and display of radius image (only in non-component mode).
calcRecall(int, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures: Calculates the recall value from given true positives and false negatives.
calcRegionAverageIntensities() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Calculates the average region intensities.
CalcSegmentationStatistics - Class in de.unihalle.informatik.MiToBo.segmentation.basics: Operator for doing statistical calculations on segmentations of images.
CalcSegmentationStatistics() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Default constructor without arguments.
CalcSegmentationStatistics(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Default constructor.
CalcSegmentationStatistics(MTBImage, MTBSegmentationInterface) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Default constructor.
CalcSegmentationStatistics(MTBImage, MTBSegmentationInterface, Vector<CalcSegmentationStatistics.CalcTargets>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Default constructor.
CalcSegmentationStatistics.CalcTargets - Enum in de.unihalle.informatik.MiToBo.segmentation.basics: Statistical numbers provided by this class.
calcSkeletonBranchFeatures - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Flag to turn on/off calculation of skeleton branch features.
calcSnakeDomain() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Calculates snake bounding box (in non-normalized coordinates!).
calcSnakeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy: Calculates total snake energy.
calcSnakeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Calculates total snake energy.
calcSolidity - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Flag to turn on/off calculation of solidity.
CalcStructureStatistics - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation: Extracts statistics from cell and structure segmentation results.
CalcStructureStatistics() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Default constructor.
CalcStructureStatistics(MTBImageByte, MTBImageByte, MTBImageByte, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Deprecated.
CalcStructureStatistics(MTBImageByte, MTBImageByte, MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Default constructor.
CalcStructureStatistics.StructureCountMode - Enum in de.unihalle.informatik.MiToBo.segmentation.evaluation: Mode how to assign structures to cell regions.
calcSurfArea - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
calcSurfArea() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
CalcTargets() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics.CalcTargets
calcTexturalEntropy(Double[][]) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
calcThreshold(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu: Calculate Otsu threshold on given image.
calcThreshold(MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu: Calculate Otsu threshold on given histogram.
calcTStD(double, double) - Static method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Calculates the threshold for the local standard daviation.
calculateConcavityData() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Extracts average concavity and standard deviation of concavities.
calculateConvexHullMeasures() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Calculates convex hull convexities and roundnesses.
calculateConvexHulls() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Calculates convex hull areas and perimeters.
calculateCovarianceMatrixAndEigenstuff() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Calculates covariance matrix and eigenvalues and -vectors.
calculateCurvatureBeusTiu(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
calculateCurvatureModifiedFreemanDavis(Vector<Point2D.Double>, int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Calculates the curvatures by a modified version of the Freeman and Davis curvature estimation algorithm.
calculateDistanceMatrices() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Calculates pairwise distance matrices and similarity network data.
calculateFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Performs the feature calculation.
calculateFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorEigenStructures
calculateFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorTiles
calculateMeanFreeData() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Computes the average data vector and makes data mean-free.
calculatePairwiseDistances() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Calculates pairwise Euclidean distances between all feature vectors.
calculatePointLineDistance(double, double, double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet: Calculates the distance between a point and a line.
calculateRegionFeatures(MTBRegion2DSet, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Extracts features for all detected and valid cell regions.
calculateSolidityValues() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Calculates solidity values.
calcVariance(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Returns the variance of an array of double.
calcVolume - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
calcVolume() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
calibration - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: calibration object (from ImageJ)
callbackArea() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Callback function called in case of changes of parameter MorphologyAnalyzer2D.calcArea.
callbackConcavity() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Callback function called in case of changes of parameter MorphologyAnalyzer2D.calcConcavityData.
callbackCurvature() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Callback function called in case of changes of parameters MorphologyAnalyzer2D.analyzeProtrusionsIndentations or MorphologyAnalyzer2D.calcMarginRoughness.
callbackInputDir() - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Callback function called in case of changes of parameter LabelImageEditor.inputDir.
callbackSolidity() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Callback function called in case of changes of parameter MorphologyAnalyzer2D.calcSolidity.
callBackUpdateSigmaThresholds() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Calculates values for mandatory parameters StegerRidgeDetection2DWrapper.sigma, StegerRidgeDetection2DWrapper.upperThresh and StegerRidgeDetection2DWrapper.lowerThresh from optional parameters StegerRidgeDetection2DWrapper.lineWidth, StegerRidgeDetection2DWrapper.highContrast and StegerRidgeDetection2DWrapper.lowContrast in case that one of the values changed.
calledFirstTime - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Flag to ensure that callback only works once the operator has been called.
callingOperator - Variable in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
callNeuriteScript(String, String) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Call a specified R script for neurite calculations.
callNeuriteSrcipt(Rengine, String, String[]) - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Call a specified R script for neurite calculations.
calStDI(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Calculates the standard deviation of the given image.
candidateRegions - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: List of stromule candidate regions.
candidates - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
canvas - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame: Canvas used by ImageJ to display the image.
categoryColors - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Color map for category colors in plot.
categoryColors - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Color map for category colors in plot.
categoryCount - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Local variable to store number of categories.
cb - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
cbbox - Variable in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel: container for arrangement of checkboxes
cbs - Variable in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel: checkbox components
cdf - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution: cumulative distribution function, used for sampling
cDOF - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory: degrees of freedom of the continuous variables of a single state
CellBoundaryExtractor2D - Class in de.unihalle.informatik.MiToBo.apps.cells2D: Operator for segmenting cell boundaries in microtubuli experiments.
CellBoundaryExtractor2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Default constructor.
CellBoundaryExtractor2D.BorderBackgroundContrast - Enum in de.unihalle.informatik.MiToBo.apps.cells2D: Border color.
CellBoundaryExtractor2D.OperationMode - Enum in de.unihalle.informatik.MiToBo.apps.cells2D: Operation mode of the operator.
cellChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Channel for cell boundary detection.
CellCntrMarker - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes: Class to represent a single marker in the image.
CellCntrMarker() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Creates a new instance of marker class.
CellCntrMarker(int, int, int, CellCntrMarkerShape) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Constructor with given coordinates and shape.
CellCntrMarkerShape - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes: Class to represent the geometric shape of a single marker in the image.
CellCntrMarkerShape() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape
CellCntrMarkerShapeCurve - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes: Class using a parametric curve as shape for markers.
CellCntrMarkerShapeCurve() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeCurve: Default constructor, it's protected to avoid constructing objects without curve data.
CellCntrMarkerShapeCurve(MTBQuadraticCurve2D) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeCurve: Default constructor with parametric curve object.
CellCntrMarkerShapeLine - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes: Class using a line segment as shape for markers.
CellCntrMarkerShapeLine() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine: Default constructor, it's protected to avoid constructing objects without curve data.
CellCntrMarkerShapeLine(Point2D.Double, Point2D.Double) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine: Default constructor.
CellCntrMarkerShapePolygon - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes: Class using a polygon as shape for markers.
CellCntrMarkerShapePolygon() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapePolygon: Default constructor, it's protected to avoid constructing objects without polygon data.
CellCntrMarkerShapePolygon(MTBPolygon2D) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapePolygon: Default constructor with region object.
CellCntrMarkerShapeRegion - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes: Class using a region as shape for markers.
CellCntrMarkerShapeRegion() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeRegion: Default constructor, it's protected to avoid constructing objects without region data.
CellCntrMarkerShapeRegion(MTBRegion2D) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeRegion: Default constructor with region object.
CellCntrMarkerShapeRegion(MTBRegion2D, MTBBorder2D) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeRegion: Constructor with region and border object.
CellCntrMarkerVector - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes: Class to represent a set of markers of a single type.
CellCntrMarkerVector(int) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Creates a new instance of MarkerVector.
CellCntrSegResult - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes: Base class representing results of MTB_CellCounter presegmentation stage(s).
CellCntrSegResult(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult: Default constructor.
CellCntrSegResultCurves - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes: Class representing results of MTB_CellCounter presegmentation stage(s).
CellCntrSegResultCurves(MTBImage, Vector<MTBQuadraticCurve2D>) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves: Constructor.
CellCntrSegResultRegions - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes: Class representing region-based results of MTB_CellCounter presegmentation stage(s).
CellCntrSegResultRegions(MTBImage, MTBRegion2DSet, MTBBorder2DSet, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Constructor.
CellCntrSegResultRegions(MTBImage, MTBRegion2DSet) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Constructor.
cellContours - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Set of extracted regions.
cellContours - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Set of detected cell boundaries.
CellCounterDetectOperator - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators: Container base class for all detectors used in the cell counter.
CellCounterDetectOperator() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Constructor.
CellCounterDetectOperatorConfigWin - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators: Deprecated.
CellCounterDetectOperatorConfigWin(ALDOperator) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Constructs a control frame for an operator object.
CellCounterDetectOperatorParticlesUWT - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators: Cell counter detector for detecting plastids.
CellCounterDetectOperatorParticlesUWT() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT: Constructor.
CellCounterDetectOperatorStromules - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators: Detector wrapper for detection of stromules from given plastid regions.
CellCounterDetectOperatorStromules() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules: Constructor.
cellGroupNames - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: List of group names, filled in ActinAnalyzer2D.clusterFeatures().
cellGroupNames - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: List of group names, filled in CytoskeletonAnalyzer2D.clusterFeatures().
cellGroups - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Group-wise cell distribution data, for each group the vector contains a hash map with the following structure: - the keys of the map are given by the cell IDs of the different cells (without basename which is equal to the group name) - the values are represented again as a hash map where the keys are given by the cluster IDs and the values by the relative frequency of the corresponding cluster in the cell Example: --------- cellGroups.get(0) = < 001-01, < [c1, vc1], ..., [c6, vc6] > > ,
cellGroups - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Group-wise cell distribution data, for each group the vector contains a hash map with the following structure: - the keys of the map are given by the cell IDs of the different cells (without basename which is equal to the group name) - the values are represented again as a hash map where the keys are given by the cluster IDs and the values by the relative frequency of the corresponding cluster in the cell Example: --------- cellGroups.get(0) = < 001-01, < [c1, vc1], ..., [c6, vc6] > > ,
cellLabelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Label image of extracted cell regions.
cellLabelImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Label image of cell areas.
CellMaskFormat() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor.CellMaskFormat
CellMigrationAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D: Operator for segmenting, tracking and analyzing 2D image sequences of fluorescently labeled cells
CellMigrationAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
CellMigrationAnalyzer(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
CellSegmentationPostprocessing - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D: operator for doing common postprocessing tasks on already segmented cell images
CellSegmentationPostprocessing() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
CellSegmentationPostprocessing(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
CellSegmenter - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D: base class for cell segmentation
CellSegmenter() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
CellSegmenter(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
cellSizes - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Array indexed with snake IDs containing region sizes of snake interiors.
cellsResult - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Result for cell/cytoplasm channel.
CellTrackerBipartite - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D: This operator assigns unique labels to regions representing individual cells in the input binary image sequence
CellTrackerBipartite() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
CellTrackerBipartite(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
cellwiseDistroKeys - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Sorted list of keys in CytoskeletonAnalyzer2D.cellwiseDistros once it is filled.
cellwiseDistros - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Map of cluster distributions per cell, filled in ActinAnalyzer2D.clusterFeatures().
cellwiseDistros - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Map of cluster distributions per cell, filled in CytoskeletonAnalyzer2D.clusterFeatures().
centerX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Ellipse center in x-direction.
centerX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
centerY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Ellipse center in x-direction.
centerY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
centroid - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: The centroid of the region (not normalised by volume!)
centroids - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
chainMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Helper matrix for exchange chain extraction: 0 = unselected, 1 = selected.
changePhase(int, int, int, short) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Change a pixel/voxel to a new phase.
changePhase(int, int, short) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Change a pixel to a new phase.
channel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
channel - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
channelIdx - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
channelsAreRGB - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
channelsToCopy - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Set of image channels to copy into result stack.
chart - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton: JFreeChart object associated with the button.
chartFrame - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton: Frame to display the chart.
ChartShowButton(Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton: Constructor.
ChartShowPanel(MTBJFreeChartDataIOSwing.ChartShowButton, String) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowPanel: Constructor.
chartTitle - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Title of the chart.
chartTitle - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Title of the chart.
ChaudhuriMatchedFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic: 2D Matched filter.
ChaudhuriMatchedFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D: Default constructor.
CHECK_CHANGED_PROPERTY - Static variable in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel: property string that is fired when the state of any checkbox is changed
CheckBoxPanel - Class in de.unihalle.informatik.MiToBo.gui: A panel with a titled border and a set of checkboxes that can be reconfigured easily.
CheckBoxPanel(String) - Constructor for class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel: Constructor
checkForIncrease() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
checkMethod - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
checkNeighbor(List<Point2D.Double>, int, int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D: Test if the given neighbor is to be added to the region.
checkSelectionConsistency() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Checks if a proper set of regions is selected in ImageJ ROI manager.
checkSelectionConsistencyForLineSegments() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Checks if a proper set of ROIs convertible to line segments is selected in ImageJ ROI manager.
chi - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
childs - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: List of nodes that are childs of the given node.
circularities - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
circularities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
cl - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
classID - Static variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper: Class identifier.
classID - Static variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Class identifier.
classID - Static variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Class identifier.
classify(MTBImage, MTBImage, String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter: decide, whether the given entropy image contains an open scratch or not
classify(double[]) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
classifyLobes - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Flag to classify lobes into different type classes.
classLock - Static variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Lock variable to make singleton thread-safe.
classmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: 2D map with class labels.
classmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: 2D map with class labels.
classmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: 2D map marking the region enclosed by the snake.
classNameMapping - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Mapping of short names to class objects.
cleanNeurites(MTBNeurite2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Method to clean up the extracted neurites, due to multiple features along a NSG path or feature shifts at the start point due to different NSG lengths.
clear() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: Remove all line segments from this set.
clear() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Remove all regions from this set
clear() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Remove all regions from this set
clear() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Remove all regions from this set
clear() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Deletes all(!)
clearData() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult: Clears all data.
clearData() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves: Clears all data.
clearData() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Clears all data.
clearPanel() - Method in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel: Remove all radiobuttons from the panel.
clearPanel() - Method in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel: Remove all radiobuttons from the panel.
clearPanel() - Method in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel: Remove all entries from the panel.
clearShapeData() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Delete shape data during reset of vector.
clickedPoints - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame: List of pixels the user selected.
clone() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTree
clone() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Clone function.
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Override java.lang.Object.clone() to create and return a copy of this object.
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Override java.lang.Object.clone() to create and return a copy of this object.
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
clone() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
clone() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
clone() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
clone() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
clone() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: generate a clone of this object
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Override java.lang.Object.clone() to create and return a copy of this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D: Override java.lang.Object.clone() to create and return a copy of this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed: Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone: Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner: Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate: Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff: Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset: Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination: Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations: Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff: Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
cloneChild(MTBTreeNode, MTBTreeNode) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree: Helper function to recursively clone child nodes in a deep fashion.
cloneTargetImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Flag to enable/disable cloning of target image.
close() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Close the displayed ImagePlus
close(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
closeButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Close button.
closeButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Close button.
closeButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Button to close the configuration window.
closeGapsNativeLinks(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Method to close gaps by linking adjacent endpoints.
closeGapsNativeLinks(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Close gaps by native linkage.
closeGapsWatershed(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Method to close gaps by watershed transformation.
closestObjectPixelMap - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Map of closest object pixels for each background location.
closeWindows() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Close all windows openened by this operator (for clean-up).
closeWindows() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
closeWindows() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
closingMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
clusterFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Performs the feature clustering via Weka's kMeans algorithm.
clusterFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Performs the feature clustering via Weka's kMeans algorithm.
clusterLabels - Variable in class de.unihalle.informatik.MiToBo.clustering.KMeans: List of assigned cluster indices, starting with 1.
clusterNum - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Number of clusters to be used in feature clustering.
clusterNum - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Number of clusters to be used in feature clustering.
clusterNum - Variable in class de.unihalle.informatik.MiToBo.clustering.KMeans: Number of clusters to be used.
clutterdistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution: spatial clutter distribution
cmdTools.cellAnalysis - package cmdTools.cellAnalysis
cmdTools.mtb_imagetools - package cmdTools.mtb_imagetools
cmdTools.tracking.multitarget - package cmdTools.tracking.multitarget
cmdTools.visualization - package cmdTools.visualization
codeArrayRI - Static variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs: Array containing rotation invariant LBP codes.
codeArrayRIU - Static variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs: Array containing uniform rotation invariant LBP codes.
codeArrayRIU - Static variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapterRIU: Rotation invariant uniform LBP code array.
codec - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
codec - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
codeDistributionRI - Static variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs: Distribution of codes.
codeStack - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal: Additional code stack.
codpanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
coffset - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
CollectContoursStageOne(MTBImage, ArrayList<Integer>) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: This method collects all contour pixels for a region in a given MTBImage.
CollectContoursStageTwo(MTBImage, ArrayList<Integer>, ArrayList<ArrayList<Point>>, boolean[][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: This method implements the final stage of the contour detection.
colMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Array containing column marks.
color - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: Current color selected.
color - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Color of markers.
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet: Color to be used.
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Color or gray value to use.
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D: Color for mask, default is white.
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet: Color to be used, known colors are: red, green, blue, yellow, white
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Color value used, e.g., for color and transparent images.
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage: Color to use.
color2int(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Transforms color to integer value.
color_blue - Static variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
color_graphEdge - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Color of graph edge points.
color_graphNode - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Color of graph node points.
color_red - Static variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
color_skelBranch - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Color of pre-detected branch points.
color_skelSpecial - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Color of pre-detected special points, for example a 2x2 skeleton region.
color_skelVisitB - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Color of visited graph branch points.
color_skelVisitE - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Color of visited graph edge points.
colorArray - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Array with colors for visualization.
colorArray - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Array containing pseudo-colors for snake visualization.
ColorChannel(int, int, int) - Constructor for enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
ColorChooserPanel(Color, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: Default constructor for panel without reset button.
ColorChooserPanel(Color, ALDParameterDescriptor, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: Default constructor.
colorFG - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
colorImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Image of regions in random colors.
ColorMapperDataIOFileInPanel(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel: Default constructor.
ColorMapperInputDirectoryIOPanel(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel: Default constructor.
colorNegative - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: Color for negative values.
colorPlot() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Plots the field in colored image.
colorPositive - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: Color for positive values.
colors - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
cols - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Number of columns of the table.
columnIDs - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputData: Indices of selected column.
columnNameToIDMap - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
columnSelection - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
columnSelectionItems - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
com_x - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Center of mass in x (just sum, not normalized by area!).
com_y - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Center of mass in y (just sum, not normalized by area!).
compactFactor - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: factors needed for compactness calculation
compactnesses - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
compactnessTreshold - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Compactness threshold for components.
compare(GraphNodeID, GraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
compare(GraphNodeID, GraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
compare(TrackEvaluator.TrackObservation, TrackEvaluator.TrackObservation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
compare(TrackEvaluator.TrackSegment, TrackEvaluator.TrackSegment) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
compareTo(MTBPoint3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
compareTo(GraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
compareTo(GraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
compareTo(AssociationDistributionNN<S, T>.ObsDistance) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ObsDistance
compareTo(TrackEvaluator.TrackObservation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
compareTo(TrackEvaluator.TrackSegment) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
componentNum - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Number of sub-space components in mode ReductionMode.NUMBER_COMPONENTS.
ComponentPostprocess - Class in de.unihalle.informatik.MiToBo.morphology: Methods for post-processing components/pixels in binary images.
ComponentPostprocess() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Default constructor.
ComponentPostprocess(MTBImage, ComponentPostprocess.ProcessMode) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Default constructor.
ComponentPostprocess(MTBImage, ComponentPostprocess.ProcessMode, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Deprecated.
ComponentPostprocess(MTBImage, ComponentPostprocess.ProcessMode, int, int, int, double) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Deprecated.
ComponentPostprocess.ProcessMode - Enum in de.unihalle.informatik.MiToBo.morphology: Processing mode identifiers.
comppanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
compression - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
compression - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
compute(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_PrattsFigureOfMerit: This method implements the PRA itself for two given contours.
compute_pczAhead(MTBTreeNode, Vector<Integer>, Stack<Integer>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN: Compute probability of all possible associations of neighboring observations including their likelihood
compute_qAhead(int, int, int, int, double, MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN: Compute tree of data association prior probabilities depending on previous associations.
computeDeltas(double[]) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Return the centered angles (named delta).
ComputeDetectionErrors() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors: This method is the implementation of the Detection Errors.
computeESS() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Compute effective sample size (ESS).
computeN() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: Derive N_n^k from X, see Han et al.
computeN() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN4
computeN() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN8
ComputeOdetsCriteria() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria: This method is the implementation of Odet's criteria.
computeSigmaScales() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Compute scaling factors of noise sigma for wavelet scales (these scaling factors are estimated using a gaussian noise image with sigma=1 to measure noise in the wavelet scales)
computeSubgraphs() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning: Compute subgraphs with greedyGourmet algorithm.
computeThetas(Vector<Point2D.Double>, int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Calculate the theta angle for all contour pixels provided.
comXs - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: List of x-coordinates of centers of mass of plastid regions.
comYs - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: List of y-coordinates of centers of mass of plastid regions.
concaveness(int, int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
concavenessValues - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
concavityMaskSize - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Masksize for concavity calculations.
ConditionalDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for conditional densities, e.g. p(x|y)
condX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution: multi state condition on the density
condX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution: multi state condition on the density
confButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton: Button to display configuration window.
confEnergyButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Config button for energies.
configButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton: Configuration button.
configGUIModeLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Enable GUI components for label mode.
configGUIModeMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Enable GUI components for mask mode.
configGUIModeRegion() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Enable GUI components for region mode.
configGUIModeShape() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Enable GUI components for shape mode.
configGUIModeThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Enable GUI components for threshold mode.
configPanel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: Panel containing configuration buttons.
ConfigureSegmentationButton(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton: Constructor.
configureSnakes(double, int, double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Configures basic snake parameters.
confObj - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools: The object instance.
confWin - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel: Configuration window to show/edit loaded data.
confWin - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
confWin - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton: Collection configuration window.
confWin - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton: Configuration window.
connectivity - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Connectivity of border pixels.
connectivity - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Connectivity within resulting borders.
connectNodesCase1(MTBGraphNode<PartitGraphNodeID>, MTBGraphNode<PartitGraphNodeID>, MTBGraphNode<PartitGraphNodeID>, MTBGraphNode<PartitGraphNodeID>, boolean) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning: Connect nodes if case 1
connectorIDs - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: List of connectors the corresponding treeline is attached to.class Note: usually a treeline should only be member of one connector, only in case of conflicts there could be more.
contains(double, double, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Determines if a point lies inside a polygon or on its boundary.
contains(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Test if a point is inside the region or not.
containsImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox: Checks if the box contains an ImagePlus.
containsMTBImage() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox: Checks if the box contains a MTBImage.
containsPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D: Checks if a given point is part of the segment.
containsPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Checks if given point lies inside of the polygon.
containsPoint(MTBPolygon2D, double, double) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper: Checks if a point lies inside of the polygon.
contour - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Analyzed region contour.
Contour2DConcavityCalculator - Class in de.unihalle.informatik.MiToBo.features.contours: class for calculating concaveness of contour pixels according to the method proposed in: Fernandez, G., Kunt, M. & Zryd, J.P. (1995) A new plant image segmentation algorithm.
Contour2DConcavityCalculator() - Constructor for class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
Contour2DConcavityCalculator(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
Contour2DConcavityCalculator(MTBImage, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
Contour2DConcavityCalculator(MTBImage, MTBContour2DSet, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
Contour2DCurvatureCalculator - Class in de.unihalle.informatik.MiToBo.features.contours: Implementation of curvature estimating algorithm's for discrete curved lines in a 2D space.
Contour2DCurvatureCalculator() - Constructor for class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Default empty constructor.
Contour2DCurvatureCalculator(MTBContour2DSet) - Constructor for class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Contour2DCurvatureCalculator.Algorithm - Enum in de.unihalle.informatik.MiToBo.features.contours
ContourConverter(MTBContour2D) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter: Default constructor.
contourID - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: ID of the contour.
ContourOnLabeledComponents - Class in de.unihalle.informatik.MiToBo.segmentation.contours.extraction: Class to segment contours from a binary image using the contour following algorithm.
ContourOnLabeledComponents() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Standard constructor.
ContourOnLabeledComponents(MTBImageByte, MTBRegion2DSet, ContourOnLabeledComponents.ContourType, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Constructor.
ContourOnLabeledComponents(MTBRegion2DSet, ContourOnLabeledComponents.ContourType, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Constructor.
ContourOnLabeledComponents.ContourType - Enum in de.unihalle.informatik.MiToBo.segmentation.contours.extraction: The possible type of contours for segmentation.
contours - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
contourSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: The set of contours represented as a Vector.
contourSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI: Set of 2D contours.
contourType - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Special type of contours to calculate.
ContourType() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents.ContourType
contourWorkSet - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
contrastEnhancer - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
conv(MTBImage, MTBImage[], int) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Convolve input image with an 'a trous' kernel (zeros inserted) given the original kernel and scale j
convert(Object, Type[], Class<?>, Type[]) - Method in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
convertContourToSnake(MTBContour2D) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Converts a contour into a snake.
convertLabelImages() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Converts input images to short pixel format and optionally inverts them.
convertRangeColorToHue(ArrayToColorMapImage.RangeColor) - Static method in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: Converts given color to hue value.
convertRegionsToSnakes(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Converts the regions of a label/binary image into a set of snakes.
convertRegionToSnake(MTBRegion2D) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Converts a region into a snake.
convertToImageJRoi() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.interfaces.MTBDataExportableToImageJROI: Function to convert object to ImageJ ROI or set of ROIs.
convertToImageJRoi() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
convertToImageJRoi() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
convertToImageJRoi() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
convertToImageJRoi() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
convertType(MTBImage.MTBImageType, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Create an image of given type from this image's values.
convertType(MTBOperator, MTBImage.MTBImageType, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Create an image of given type from this image's values.
convertType(MTBImage, MTBImage.MTBImageType, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory: Create an image of given type from this image's values.
convexHullAreas - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
convexHullConvexities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
ConvexHullExtraction - Class in de.unihalle.informatik.MiToBo.morphology: operator for calculating the convex hulls of binary connected components
in a given image or of a set of regions using the Jarvis march algorithm
ConvexHullExtraction() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
ConvexHullExtraction(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
ConvexHullExtraction(MTBImage, boolean, boolean) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
ConvexHullExtraction.InputType - Enum in de.unihalle.informatik.MiToBo.morphology: Type of input to work on.
convexHullPerimeters - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
convexHullRoundnessValues - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
convexHulls - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
convolve(MTBImage, MTBImage, int[], boolean, MTBImageWindow.BoundaryPadding) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Convolve an image with a specified kernel.
coordinatesNeighborNeighbors - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: For each neighbor in the neighborhood this collection holds coordinates of all other pixels in the neighborhood which are connected to the neighbor under consideration with regard the the neighborhood definition.
coordinatesNeighborNeighborsByCoord - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: As this array gives for each neighbor in the neighborhood coordinates of its neighbors (i.e. neighborneighbors).
coordinatesNeighbors - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: For each neighbor in the neighborhood this gives their coordinates in a 3x3x3 array center around the current pixel (of which the neighborhood is represented).
CoordInt3D(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.CoordInt3D
copy() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
copy() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
copy() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetPredictionFilterIndep
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA: Not implemented, always returns null
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState: Copy this multi-state
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID
copy() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.Copyable
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
Copyable<T> - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces: Interface for objects that can be copied (deep copy is assumed).
copyInputImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Flag to enable/disable plotting directly into input image.
copyPhysicalProperties(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Copy physical properties like stepsizes and units from {#sourceImg} to this.
copyTo(MTBLevelsetFunctionPDE) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: copy this object to another one
correctDirectness(MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Method to correct the direction of every edge inside the skeleton graph from a given root node.
correctGamma - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
correctGamma(MTBImage, double, int) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Perform gamma correction to the specified channel of the input image, using the given gamma value.
correctGammaAuto(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Perform gamma correction to the specified channel of the input image.
correctPosition - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Correct the line position if it has different contrast on each side of it.
correlationImages - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Stack of correlation images for different scale combinations.
corrThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Threshold for correlation images.
corrThreshold - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT: Threshold for correlation images.
cost - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Cost of the MTBGraphEdge.
cot(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Return the cotangens of value.
count - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
counterClockwiseSnakePointOrderRequested - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Flag to indicate if snakes are required to be sorted counter-clockwise.
countInner() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Get the number of inner borders included.
countMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Mode for assigning structures to regions.
cov - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution: covariance matrix
covs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
cparticles - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
create2DTrajectoryImage(boolean, boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
create3DTrajectoryImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
createChart(CategoryDataset) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Creates the chart.
createChart(CategoryDataset) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Creates the chart.
createCircularElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
createColor(int) - Static method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Returns a marker color according to given type ID.
createColorImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Flag to enable/disable creation of region image in random colors.
createContourOverlay - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
createCurvatureInfoImage - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Flag to enable drawing curvature information to info image.
createDataAssociation() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusiveFactory
createDataAssociation(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusiveFactory
createDataAssociation() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociationFactory: Create a new data association object
createDataAssociation(int, int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociationFactory: Create a new data association object for given number of targets/states and observations
createDataset() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Create the dataset from the given input data.
createDataset() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Create the dataset from input data.
createDynamicModels() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
createEmptyMultiState() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory: Create an empty multi state object
createEmptyMultiState() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiStateFactory
createEnergy(MTBLevelsetMembership, double) - Static method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE: Create a proper length energy asked for by the level set function.
createEnergy(MTBImage, MTBLevelsetMembership, double) - Static method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE: Create a proper length energy asked for by the level set function.
createFloatImage - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Create byte or float image
createGaussianNoiseImage(double, double, double, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Create an image with Gaussian noise
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing: Generic reading of table models.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBWrapperDataIOSwing
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing: GUI element for reading sets of snake energies.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing: Generic reading of segmentation objects.
createHorizontalLineElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
createIDImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Flag to enable/disable creation of gray-scale image with region IDs.
createImageFromWindow() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
createInitBar(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter: create rectangular shaped bar as initialization for the scratch
createInitialStates() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
createLabelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Flag to enable/disable creation of gray-scale label image.
createMasks - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Flag to enable binary mask creation.
createMTBImage(ImagePlus) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Factory method to create MTBImage objects.
createMTBImage(int, int, int, int, int, MTBImage.MTBImageType) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Factory method to create MTBImage objects with value 0 at each coordinate.
createMTBImageByte(int, int, int, int, int, byte[][]) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Creates an image of type MTBImage.MTBImageType.MTB_BYTE from the given data array.
createMultiState(double[][], T[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory: Create a multi state object initialized by the specified data
createMultiState(Matrix[], T[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory: Create a multi state object initialized by the specified data
createMultiState(double[][], T[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiStateFactory
createMultiState(Matrix[], T[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiStateFactory
createObservationModel() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
createOverlay() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
createOverlayImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
createProgressionImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
createQuadraticElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
createRandomRegion2D(int, int, int, Random) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Create a random connected 2D region of size maxArea in a hypothetical image of a random size between 1 and maxArea.
createRectangularElement(int, int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
createRengine() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Method to generate a R thread inside the java application.
createRengine() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Method to generate a R thread inside the java application.
createResultDir(String) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Create directory where all results will be stored.
createResultTable(Vector<Vector<Integer>>) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Create result table with statistics about nuclei and particles.
createResultTable() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: This method prepares the result table for the solution.
createSeedRegions(MTBImageByte, int, int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Create seed regions from the intial segmentation.
createSkeletonInfoImage - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Flag to enable drawing skeleton information to info image.
createSwapResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Create result table with statistics about nuclei and particles.
createVerticalLineElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
CropImage - Class in de.unihalle.informatik.MiToBo.tools.image: Crop an image part.
CropImage() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.CropImage: Constructor.
cSize - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Size of input image in c dimension.
cSnakeOpt - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Reference to a coupled snake optimizer.
cSnakeOpt - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Reference to a coupled snake optimizer.
csvFile - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter: Output file name.
ctrPoints - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
cumulate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: calculate the cumulative histogram
cumulatedObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency: cumulated number of previous observations for each time step, required to determine the individual array sizes in the adjacency matrix
cumulateOnly() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: calculate the cumulative histogram without changing the sum of absolute frequencies (normalizing factor), because cumulate() calls initialize() and thus destroys this normalizing factor
CURRENT_TYPE - Static variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
currentFile - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Full path name of currently active image file.
currentIndex - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator: Index of iterator in set.
currentIndexCol - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator: Index of iterator in set.
currentIndexRow - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator: Index of iterator in set.
currentInput - Static variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get initial directory from environment configuration.
currentInput - Static variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Get initial directory from environment configuration.
currentMaskShape - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology: shape of mask if mask !
currentMaskSize - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology: mask size of mask if mask !
currentMax - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
currentOverlapMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Overlap mask of current snake configuration, updated in each iteration.
currentSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Current set of snakes.
currentSnk - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Current snake the energy is based on.
curvatureInfoImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Info image for curvature analysis.
curve - Variable in class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet: Estimated curve.
curve - Variable in class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet: Estimated curve.
curveType - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Type of curve.
CurveType() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.CurveType
cweights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
cytoChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Channel of input image containing stained cytoskeleton.
cytoDetector - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Cytoplasma detection operator.
CytoplasmAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.cytoplasm2D: Operator to segment cell contours from a given single-layer image.
CytoplasmAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Default constructor.
CytoplasmAnalyzer2D(MTBImage, MTBPolygon2DSet, SnakeOptimizerCoupled, CytoplasmAnalyzer2D.DetectMode, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Default constructor.
CytoplasmAnalyzer2D.DetectMode - Enum in de.unihalle.informatik.MiToBo.apps.cytoplasm2D: Operator mode.
cytoSkelChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Channel of input image containing stained cytoskeleton.
CytoskeletonAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton: Operator for extracting quantative global features of the cytoskeleton.
CytoskeletonAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Default constructor.
CytoskeletonFeatureExtractor - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton: Operator for extracting features for the ActinAnalyzer2D.
CytoskeletonFeatureExtractor() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Default constructor.
CytoskeletonFeatureExtractor.CellMaskFormat - Enum in de.unihalle.informatik.MiToBo.apps.cytoskeleton: Format of cell segmentation data.
CytoskeletonFeatureExtractorEigenStructures - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton: Operator for extracting Eigen structures as features for the ActinAnalyzer2D.
CytoskeletonFeatureExtractorEigenStructures() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorEigenStructures: Default constructor.
CytoskeletonFeatureExtractorHaralickMeasures - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton: Operator for extracting Haralick texture measures from co-occurrence matrices as features for the ActinAnalyzer2D.
CytoskeletonFeatureExtractorHaralickMeasures() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures: Default constructor.
CytoskeletonFeatureExtractorLBPs - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton: Operator for extracting LBP features for the ActinAnalyzer2D.
CytoskeletonFeatureExtractorLBPs() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPs: Default constructor.
CytoskeletonFeatureExtractorLBPsRIU - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton: Operator for extracting LBP RIU features for the ActinAnalyzer2D.
CytoskeletonFeatureExtractorLBPsRIU() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPsRIU: Default constructor.
CytoskeletonFeatureExtractorTiles - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton: Operator for extracting features for the ActinAnalyzer2D.
CytoskeletonFeatureExtractorTiles() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorTiles: Default constructor.

D

d - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Implicit curve parameter d.
darkLine - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: If true, dark lines on bright background are extracted.
data - Variable in class de.unihalle.informatik.MiToBo.clustering.KMeans: Data to be clustered.
data - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel: Currently loaded data set.
data - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton: Data to be displayed.
data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: MTBGraphNode data.
data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: Array holding the histogram data
data - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter: Data to save to file.
data - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel: The data contained in the table.
data - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Data to display.
data - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Data to display.
DataAssociation - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces: Interface for data association objects.
DataAssociationExclusive - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl: A class that represents exlusive data association.
DataAssociationExclusive() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive: Constructor
DataAssociationExclusiveFactory - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl: Factory class for exclusive data association objects
DataAssociationExclusiveFactory() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusiveFactory
DataAssociationFactory - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces: Interface for data association object factories
DataConverter<S,T> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatools: An operator class to convert between data types.
DataConverter() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
dataDim - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Dimensionality of the input data.
dataIsPeriodic - Variable in class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D: Flag to indicate if data is periodic.
dataObject - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: Data object associated with the given node.
dataset - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Input data with each column containing a data vector.
DataTabFileFilter() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components.MTBTableWindow.DataTabFileFilter
DatatypeExceptionType() - Constructor for enum de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException.DatatypeExceptionType
db - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
dbf - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
DE - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Check if you want to compute the Detection Errors
de.unihalle.informatik.MiToBo.apps.biofilms - package de.unihalle.informatik.MiToBo.apps.biofilms
de.unihalle.informatik.MiToBo.apps.cellMorphology - package de.unihalle.informatik.MiToBo.apps.cellMorphology
de.unihalle.informatik.MiToBo.apps.cells2D - package de.unihalle.informatik.MiToBo.apps.cells2D
de.unihalle.informatik.MiToBo.apps.cytoplasm2D - package de.unihalle.informatik.MiToBo.apps.cytoplasm2D
de.unihalle.informatik.MiToBo.apps.cytoskeleton - package de.unihalle.informatik.MiToBo.apps.cytoskeleton: Provides tools and applications for quantifying actin filament structures in microscopy images of cells.
de.unihalle.informatik.MiToBo.apps.datatypes.cellImages - package de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes - package de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes
de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation - package de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation
de.unihalle.informatik.MiToBo.apps.minirhizotron.utils - package de.unihalle.informatik.MiToBo.apps.minirhizotron.utils
de.unihalle.informatik.MiToBo.apps.neurites2D - package de.unihalle.informatik.MiToBo.apps.neurites2D
de.unihalle.informatik.MiToBo.apps.neurons2D - package de.unihalle.informatik.MiToBo.apps.neurons2D
de.unihalle.informatik.MiToBo.apps.nuclei2D - package de.unihalle.informatik.MiToBo.apps.nuclei2D
de.unihalle.informatik.MiToBo.apps.particles2D - package de.unihalle.informatik.MiToBo.apps.particles2D
de.unihalle.informatik.MiToBo.apps.plantCells.plastids - package de.unihalle.informatik.MiToBo.apps.plantCells.plastids
de.unihalle.informatik.MiToBo.apps.plantCells.stromules - package de.unihalle.informatik.MiToBo.apps.plantCells.stromules
de.unihalle.informatik.MiToBo.apps.scratchAssay - package de.unihalle.informatik.MiToBo.apps.scratchAssay
de.unihalle.informatik.MiToBo.apps.singleCellTracking2D - package de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
de.unihalle.informatik.MiToBo.apps.xylem - package de.unihalle.informatik.MiToBo.apps.xylem
de.unihalle.informatik.MiToBo.clustering - package de.unihalle.informatik.MiToBo.clustering
de.unihalle.informatik.MiToBo.color.conversion - package de.unihalle.informatik.MiToBo.color.conversion
de.unihalle.informatik.MiToBo.color.tools - package de.unihalle.informatik.MiToBo.color.tools
de.unihalle.informatik.MiToBo.core.batch.provider.input.swing - package de.unihalle.informatik.MiToBo.core.batch.provider.input.swing
de.unihalle.informatik.MiToBo.core.batch.provider.output.swing - package de.unihalle.informatik.MiToBo.core.batch.provider.output.swing
de.unihalle.informatik.MiToBo.core.dataconverter - package de.unihalle.informatik.MiToBo.core.dataconverter
de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline - package de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
de.unihalle.informatik.MiToBo.core.dataio.provider.swing - package de.unihalle.informatik.MiToBo.core.dataio.provider.swing
de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components - package de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components
de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans - package de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
de.unihalle.informatik.MiToBo.core.datatypes - package de.unihalle.informatik.MiToBo.core.datatypes: Provides basic datatypes for MiToBo.
de.unihalle.informatik.MiToBo.core.datatypes.defines - package de.unihalle.informatik.MiToBo.core.datatypes.defines
de.unihalle.informatik.MiToBo.core.datatypes.images - package de.unihalle.informatik.MiToBo.core.datatypes.images: Contains MiToBo image data types.
de.unihalle.informatik.MiToBo.core.datatypes.interfaces - package de.unihalle.informatik.MiToBo.core.datatypes.interfaces
de.unihalle.informatik.MiToBo.core.datatypes.neurites - package de.unihalle.informatik.MiToBo.core.datatypes.neurites
de.unihalle.informatik.MiToBo.core.datatypes.wrapper - package de.unihalle.informatik.MiToBo.core.datatypes.wrapper: Provides wrapper for for input and output datatypes for MiToBo operators.
de.unihalle.informatik.MiToBo.core.exceptions - package de.unihalle.informatik.MiToBo.core.exceptions: Defines MiToBo exceptions.
de.unihalle.informatik.MiToBo.core.grappa - package de.unihalle.informatik.MiToBo.core.grappa
de.unihalle.informatik.MiToBo.core.gui - package de.unihalle.informatik.MiToBo.core.gui
de.unihalle.informatik.MiToBo.core.helpers - package de.unihalle.informatik.MiToBo.core.helpers
de.unihalle.informatik.MiToBo.core.imageJ - package de.unihalle.informatik.MiToBo.core.imageJ: Provides convenience classes for interaction with ImageJ system.
de.unihalle.informatik.MiToBo.core.operator - package de.unihalle.informatik.MiToBo.core.operator: Provides basis classes for MiToBo operator concept.
de.unihalle.informatik.MiToBo.enhance - package de.unihalle.informatik.MiToBo.enhance: Provides classes for image preprocessing and improvement (no filters!).
de.unihalle.informatik.MiToBo.features - package de.unihalle.informatik.MiToBo.features: Provides operators for calculating features from given images, e.g., statistical indicators or texture measures.
de.unihalle.informatik.MiToBo.features.contours - package de.unihalle.informatik.MiToBo.features.contours
de.unihalle.informatik.MiToBo.features.regions - package de.unihalle.informatik.MiToBo.features.regions
de.unihalle.informatik.MiToBo.features.statistical - package de.unihalle.informatik.MiToBo.features.statistical: Provides operators for calculating statistical image features, e.g., average intensities or variances, or moments of the intensity distribution.
de.unihalle.informatik.MiToBo.features.texture - package de.unihalle.informatik.MiToBo.features.texture: Provides operators for calculating texture features from given images, e.g., Haralick measures.
de.unihalle.informatik.MiToBo.features.texture.lbp - package de.unihalle.informatik.MiToBo.features.texture.lbp
de.unihalle.informatik.MiToBo.fields - package de.unihalle.informatik.MiToBo.fields: Provides classes for calculating gradient vector flow fields, image gradient fields, potential fields and other possible fields from different data sources.
de.unihalle.informatik.MiToBo.filters.linear - package de.unihalle.informatik.MiToBo.filters.linear: Provides classes implementing linear systems.
de.unihalle.informatik.MiToBo.filters.linear.anisotropic - package de.unihalle.informatik.MiToBo.filters.linear.anisotropic
de.unihalle.informatik.MiToBo.filters.nonlinear - package de.unihalle.informatik.MiToBo.filters.nonlinear: Provides classes implementing nonlinear image filters.
de.unihalle.informatik.MiToBo.filters.vesselness - package de.unihalle.informatik.MiToBo.filters.vesselness: Provides various operators for enhancing vessel-like structures in images.
de.unihalle.informatik.MiToBo.gui - package de.unihalle.informatik.MiToBo.gui
de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes - package de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes
de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators - package de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators
de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml - package de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml
de.unihalle.informatik.MiToBo.io.dirs - package de.unihalle.informatik.MiToBo.io.dirs: Provides classes for dealing with directories.
de.unihalle.informatik.MiToBo.io.files - package de.unihalle.informatik.MiToBo.io.files: Provides classes for handling (non-)image files.
de.unihalle.informatik.MiToBo.io.images - package de.unihalle.informatik.MiToBo.io.images: Provides classes for handling image files.
de.unihalle.informatik.MiToBo.io.importer - package de.unihalle.informatik.MiToBo.io.importer
de.unihalle.informatik.MiToBo.io.tools - package de.unihalle.informatik.MiToBo.io.tools: Contains helper classes for image I/O.
de.unihalle.informatik.MiToBo.math - package de.unihalle.informatik.MiToBo.math: Provides mathematical functionality.
de.unihalle.informatik.MiToBo.math.arrays.filter - package de.unihalle.informatik.MiToBo.math.arrays.filter
de.unihalle.informatik.MiToBo.math.distributions.impl - package de.unihalle.informatik.MiToBo.math.distributions.impl
de.unihalle.informatik.MiToBo.math.distributions.interfaces - package de.unihalle.informatik.MiToBo.math.distributions.interfaces
de.unihalle.informatik.MiToBo.math.fitting - package de.unihalle.informatik.MiToBo.math.fitting
de.unihalle.informatik.MiToBo.math.graphs - package de.unihalle.informatik.MiToBo.math.graphs
de.unihalle.informatik.MiToBo.math.images - package de.unihalle.informatik.MiToBo.math.images: Provides mathematical operations on images.
de.unihalle.informatik.MiToBo.math.optimization - package de.unihalle.informatik.MiToBo.math.optimization
de.unihalle.informatik.MiToBo.math.statistics - package de.unihalle.informatik.MiToBo.math.statistics: This package contains oeprators for performing statistical analysis of data sets.
de.unihalle.informatik.MiToBo.morphology - package de.unihalle.informatik.MiToBo.morphology: Provides classes for morphological processing of binary images.
de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes - package de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
de.unihalle.informatik.MiToBo.segmentation.activecontours.energies - package de.unihalle.informatik.MiToBo.segmentation.activecontours.energies
de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions - package de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions
de.unihalle.informatik.MiToBo.segmentation.basics - package de.unihalle.informatik.MiToBo.segmentation.basics
de.unihalle.informatik.MiToBo.segmentation.contours.extraction - package de.unihalle.informatik.MiToBo.segmentation.contours.extraction: Provides classes for performing contour extractions from regions or other image elements.
de.unihalle.informatik.MiToBo.segmentation.evaluation - package de.unihalle.informatik.MiToBo.segmentation.evaluation
de.unihalle.informatik.MiToBo.segmentation.evaluation.measures - package de.unihalle.informatik.MiToBo.segmentation.evaluation.measures
de.unihalle.informatik.MiToBo.segmentation.helpers - package de.unihalle.informatik.MiToBo.segmentation.helpers
de.unihalle.informatik.MiToBo.segmentation.levelset.core - package de.unihalle.informatik.MiToBo.segmentation.levelset.core
de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable - package de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable
de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE - package de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes - package de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes
de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver - package de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver
de.unihalle.informatik.MiToBo.segmentation.regions.convert - package de.unihalle.informatik.MiToBo.segmentation.regions.convert
de.unihalle.informatik.MiToBo.segmentation.regions.filling - package de.unihalle.informatik.MiToBo.segmentation.regions.filling: Provides operators for filling wholes in binary 2D/3D regions.
de.unihalle.informatik.MiToBo.segmentation.regions.labeling - package de.unihalle.informatik.MiToBo.segmentation.regions.labeling: Provides classes to perform region labeling to find connected components in binarized images.
de.unihalle.informatik.MiToBo.segmentation.regions.mser - package de.unihalle.informatik.MiToBo.segmentation.regions.mser
de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes - package de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes: Provides basic datatypes for MiToBo explicit active contours (snakes).
de.unihalle.informatik.MiToBo.segmentation.snakes.energies - package de.unihalle.informatik.MiToBo.segmentation.snakes.energies: Provides classes with energies to be used with MiToBo snakes.
de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt - package de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt: Provides classes with parameter adaptation for energies to be used with MiToBo snakes.
de.unihalle.informatik.MiToBo.segmentation.snakes.optimize - package de.unihalle.informatik.MiToBo.segmentation.snakes.optimize: Provides classes for performing snake-based segmentation on images.
de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize - package de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize: Provides classes for calculating several update strategies of the snake step size gamma.
de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination - package de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination: Provides classes for calculating several termination strategies of the snake optimization.
de.unihalle.informatik.MiToBo.segmentation.thresholds - package de.unihalle.informatik.MiToBo.segmentation.thresholds: Provides classes for thresholding grayscale and color images.
de.unihalle.informatik.MiToBo.tools - package de.unihalle.informatik.MiToBo.tools
de.unihalle.informatik.MiToBo.tools.image - package de.unihalle.informatik.MiToBo.tools.image
de.unihalle.informatik.MiToBo.tools.interactive - package de.unihalle.informatik.MiToBo.tools.interactive
de.unihalle.informatik.MiToBo.tools.strings - package de.unihalle.informatik.MiToBo.tools.strings
de.unihalle.informatik.MiToBo.tools.system - package de.unihalle.informatik.MiToBo.tools.system
de.unihalle.informatik.MiToBo.topology - package de.unihalle.informatik.MiToBo.topology
de.unihalle.informatik.MiToBo.tracking.multitarget.algo - package de.unihalle.informatik.MiToBo.tracking.multitarget.algo
de.unihalle.informatik.MiToBo.tracking.multitarget.datatools - package de.unihalle.informatik.MiToBo.tracking.multitarget.datatools
de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts - package de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts
de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl - package de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces - package de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces
de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts - package de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl - package de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
de.unihalle.informatik.MiToBo.tracking.multitarget.eval - package de.unihalle.informatik.MiToBo.tracking.multitarget.eval
de.unihalle.informatik.MiToBo.transforms - package de.unihalle.informatik.MiToBo.transforms
de.unihalle.informatik.MiToBo.visualization.colormappings - package de.unihalle.informatik.MiToBo.visualization.colormappings
de.unihalle.informatik.MiToBo.visualization.drawing - package de.unihalle.informatik.MiToBo.visualization.drawing: Provides operators to visualize data types.
de.unihalle.informatik.MiToBo.visualization.plots - package de.unihalle.informatik.MiToBo.visualization.plots
debug - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
debug - Variable in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
debug - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Debug flag for internal use only.
debug - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
debug - Variable in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame: Debug flag (not accessible from outside).
debug - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Local flag for debug output.
debug - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline: Debugging output
debug - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
debug - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
debug - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Bit mask for debug output on System.out.
debug - Static variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime: For internal use.
debug - Static variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: debug flag
debugInfoImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper: Debug image to visualize analysis results.
debugReport(String) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
decrease - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed: Fixed decrease factor for adaptation of all gamma values.
DEFAULT_ALPHA - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
DEFAULT_erodeSize - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Default size of the structuring element to erode the image
DEFAULT_FALL_BACK - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
DEFAULT_hueThresh - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Default hue threshold
DEFAULT_KAPPA - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
DEFAULT_LAMBDA_BG - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
DEFAULT_LAMBDA_FG - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
DEFAULT_linkageMode - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Default linkage mode for growing
DEFAULT_MAXITER - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
DEFAULT_minAreaAfterOpening - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
DEFAULT_minAreaPostProcessing - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Minimum area of a region in post processing.
DEFAULT_minAreaSeedRegions - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Default minimum area for a region to be further eroded
DEFAULT_minCompactness - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
DEFAULT_MU - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
DEFAULT_neighbourhood - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Default neighborhood for growing
DEFAULT_NU - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
DEFAULT_openingSESize - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Default size of structuring element for opening (post processing)
DEFAULT_satThresh - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Default saturation threshold
DEFAULT_seOpeningSize - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
DEFAULT_SIGMA - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
DEFAULT_xThresh - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Default intensity threshold
defaultDirections - Static variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures: Default directions for Haralick features.
defaultfps - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
degree - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
DEGREE_TO_BYTE - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
degSampling - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Sampling step size for vesselness enhancement filtering.
deleteRegionFromImage(MTBImageByte, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Set pixels of the points contained in the given region to 0(zero).
delim - Variable in class de.unihalle.informatik.MiToBo.io.importer.GetMTBContour2DSetFromXSVFiles: Delimiter in xSV files.
delimiter - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Delimiter to be used when exporting the model.
delta - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: X- and Y-coordinate differences of the 8-way neighbors.
delta - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Difference between threshold levels to compare.
delta_t - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
delta_t - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
delta_t - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
DeltaApproxHelper - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core: Class calculating approximations to the Dirac impulse function.
DeltaApproxHelper(double, DeltaApproxHelper.ApproxVersion) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper: Default constructor.
DeltaApproxHelper.ApproxVersion - Enum in de.unihalle.informatik.MiToBo.segmentation.levelset.core: Available approximations for the Heaviside function and its derivatives.
deltaApproximator - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives: Helper to calculate approximated values for the Dirac function.
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Calculate differences of energy if the pixel/voxel (x,y,z) is changed from its current phase in the level set function phi supplied from current phase to newPhase.
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Calculate differences of energy if the pixel/voxel (x,y,z) changes its phase in the levelest function phi supplied as argument and assumed to be associated with this energy object.
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
deltaHelper - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area: Helper object for calculating approximated values of Heaviside function.
deltaHelper - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit: Helper object to calculate values of approximated function.
deltaHelper - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length: Helper object for calculating approximated values of Heaviside function.
deltaT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
deltaT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
deltaT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
deltaT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
deltaT - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives: Time step size in iterative optimization.
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
deltaX - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
deltaXY - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
deltaXY - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper: Physical pixel resolution.
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
deltaY - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
deltaZ - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
deltaZ - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
denoise - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
denoise(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Denoise wavelet coefficients using Jeffrey's noninformative prior for a given sigma of noise
denoiseDWTJeffreys(MTBImage[], double, double[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Denoise wavelet coefficients using Jeffrey's noninformative prior [..]
denormalize() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Denormalizes the snake coordinates.
depth - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: Depth of segmentation domain.
depth - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Depth of the input image and levelset function.
depth - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Depth of the input image.
depthFirstSearch(Vector<Point2D.Double>, Vector<Integer>, MTBNeuriteSkelGraphNode<Point2D.Double>, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Depth-first-search to collect data from the neurite skeleton graph in a SWC file like format.
desiredImageClass - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing: Class of image to be returned.
destinationImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
detectedBorders - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult: Set of pre-segmented borders.
detectedNeurites - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Vector of detected neurite sets for each image.
detectedNeuritesSet - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Final set of detected neurites.
detectedParticles - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
detectedRegions - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Set of pre-segmented regions.
detectedRegions - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
detectedStomata - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves: Set of pre-segmented regions.
detectionChannel - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
detectionChannel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
detectionMode - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Operator mode to run.
detectionResultTable - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
detectionResultTable - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
DetectMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D.DetectMode
DetectMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D.DetectMode
DetectMSERs - Class in de.unihalle.informatik.MiToBo.segmentation.regions.mser: Implementation of maximally stable extremal regions based on ImgLib2.
DetectMSERs() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Default constructor.
DetectMSERs.Thresholding_Direction - Enum in de.unihalle.informatik.MiToBo.segmentation.regions.mser: Modes for direction of intensity thresholding.
DetectorExternalEnergy() - Constructor for enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos.DetectorExternalEnergy
detectorMode - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
detectProtrusionsIndentations(MTBContour2D, MorphologyAnalyzer2DInProData, double[], int, int) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper: Method to detect significant indentations and protrusions along contour.
detectResults - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Detection result.
detectStromuliRidgeModel(MTBImageShort, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Detect stromule candidates applying Steger operator.
detectStromuliStatisticalModel(MTBImageShort, MTBImage, double[], double[], double[]) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Detect stromules applying a statistical model.
detectWithLocalContrastEnhancement() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Detect nuclei by first improving image contrast.
detectWithNiblack() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Detects nuclei based on Niblack thresholding.
detectWithOtsu_erodedilate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Detects nuclei based on Otsu thresholding and a combination of erosion/ dilation.
detectWithOtsu_openclose() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Detects nuclei based on Otsu thresholding and a combination of opening and closing.
detectZSlice - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Index of input image slice if z-stack is provided as input.
determineGatingDistance() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite: automatic gating distance determination according to:

"Automated and semi-automated cell tracking: addressing portability challenges"
KAN, A. and CHAKRAVORTY, R. and BAILEY, J. and LECKIE, C. and MARKHAM, J. and DOWLING, M.R.
determineSubspaceDimension() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Determines desired sub-space dimensionality according to selected mode.
determineTypeOfCurve() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Figure out which kind of curve we have.
diagonalNeighbors - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Flag for using 8-neighborhood.
diagonalNeighbors - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Flag to define 4-/8-neighborhood in components.
diameter - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
DijkstraShortestPixelPathFinder - Class in de.unihalle.informatik.MiToBo.math.graphs: Search shortest path between two pixels in an image using Dijkstra.
DijkstraShortestPixelPathFinder() - Constructor for class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Default constructor.
DijkstraShortestPixelPathFinder.GraphNode - Class in de.unihalle.informatik.MiToBo.math.graphs: Local class to represent the nodes of the graph.
DijkstraShortestPixelPathFinder.WeightModel - Enum in de.unihalle.informatik.MiToBo.math.graphs: Modes how to set the weights.
dilate(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
dilate1D(double[], int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
dilateComponentsTopologyPreserving(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Perform a dilation of the given image with given masksize, but preserve topology.
dilateMaskSize - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Mask size for topology-preserving dilation.
dilationAreas - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
dimension - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: Dimension of image
dirac_v1(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper: Implements version 1 of approximation.
dirac_v2(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper: Implements version 2 of approximation.
directed - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: True if MTBGraph is directed.
directed - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
directions - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures: Directions for calculating cooccurrence matrices.
directions - Variable in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures: Directions.
directoryDefault - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel: Default directory to be used initially.
DirectoryTree - Class in de.unihalle.informatik.MiToBo.io.dirs: This class implements a data structure for representing directory trees.
DirectoryTree(String) - Constructor for class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree: Standard constructor.
DirectoryTree(String, boolean) - Constructor for class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree: Constructor.
DirectoryTreeNodeData - Class in de.unihalle.informatik.MiToBo.io.dirs: Implements class MTBTreeNodeData for the tree sub-class DirectoryTree.
DirectoryTreeNodeData(String) - Constructor for class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData: Default constructor.
dirLoaderPanel - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel: Panel containing elements for selecting input directory.
dirPath - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputData: Name of directory including full path.
dirProvider - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel: Provider to read input directory.
dirSelection - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel: Directory chooser.
disableComponent() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
disableComponent() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
disableComponent() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.
disableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
disableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Disables graphical elements to prohibit value changes.
disableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
disableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Deactivates the configuration window to prohibit value changes.
disabledColor - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
disableEnergyCalculation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Disable energy calculations completely.
disableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D: Disable kernel normalization.
disableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D: Disable kernel normalization.
disableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Disable kernel normalization.
disableSaveIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Do not save intermediate results.
disableSaveIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Deactivates writing of intermediate results.
disableShowIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Disable display of intermediate results.
disableShowIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Deactivates display of intermediate results.
DISAPPEARED - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
discardShortTracks() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction: delete trajectories whose length is too short
discardShortTracks() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D: delete trajectories whose length is too short
dispImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Image for displaying intermediate/final results.
dispImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Image for showing/saving intermediate results.
display - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.HistogramFrame
displayColor - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
displayEnergyButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Config button for energies.
DisplayImage - Class in cmdTools.visualization: A simple commandline tool to display image files using MiToBo's image reader.
DisplayImage() - Constructor for class cmdTools.visualization.DisplayImage
displayThres - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
displayWin - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayButton: Collection display window.
dispose() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
dispose() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
dispose() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
dispose() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
dispose() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
dispose() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
dispose() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
dispose() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
dispose() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.
dispose() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
dispose() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Releases all graphical components associcated with this provider.
dispose() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
dispose() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Disposes this window and all sub-components.
dist(MTBTopologicalNumber.Point3D) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D: Euclidean distance to pt
dist - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ObsDistance
distance - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures: Distance.
distance(Point2D.Double, Point2D.Double, double, double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
distance(MTBPoint3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Compute the Euclidean distance between this 3D point object and the given 3D point object.
distance(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Compute the Euclidean distance between this 3D point object and the given location.
distance - Variable in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures: Distance.
distanceImg - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: The distance field as MTBImage.
distanceMap - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: The distance field as two-dimensional double array.
distanceMetric - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Distance metric to apply.
DistanceMetric() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.DistanceMetric
DistanceTargetFunction(Point2D.Double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.DistanceTargetFunction: Default constructor.
DistanceTransform - Class in de.unihalle.informatik.MiToBo.morphology: Calculate Champfer distance transform with optional precursor infos.
DistanceTransform() - Constructor for class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Standard constructor.
DistanceTransform(MTBImageByte, DistanceTransform.DistanceMetric, DistanceTransform.ForegroundColor) - Constructor for class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Constructor to create a new DistanceTransform object.
DistanceTransform.DistanceMetric - Enum in de.unihalle.informatik.MiToBo.morphology: Several distance metrics.
DistanceTransform.ForegroundColor - Enum in de.unihalle.informatik.MiToBo.morphology: Color of binary image foreground.
distField - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance: The calculated 2D vector field from the distance map.
distImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Calculated distance map.
DistinctColorListGenerator - Class in de.unihalle.informatik.MiToBo.color.tools: Operator generating a list of N colors with subsequent colors being significantly different to each other.
DistinctColorListGenerator() - Constructor for class de.unihalle.informatik.MiToBo.color.tools.DistinctColorListGenerator: Default constructor.
distmet - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Metric for distance map calculation.
distMetric - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance: The used distance metric for the distance map calculation.
distroData - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Cluster distribution data, rows refer to clusters and columns to cells.
distroData - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Cluster distribution data, rows refer to clusters and columns to cells.
distroDataGroups - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Group names linked to entries in CytoskeletonAnalyzer2D.distroData.
div(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection: Method to divide two images.
div(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Divide each image value by a constant.
div(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Divide the elements of two images (img1/img2)
div(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Divide the elements of two images (img1/img2)
doc - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
doClustering(Instances) - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans: Does the actual clustering.
doDimensionReduction() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Does the actual dimension reduction by data projection into sub-space.
doErosion - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Calculates evaluation measures.
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Method to overwrite that does actual calculations.
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_HausdorffDistance
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria: This method does the actual work.
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_PrattsFigureOfMerit
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_RecallPrecisionF
DOF - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
doFeatureCalculation - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Flag for calculating features.
doFeatureCalculation - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Flag for calculating features.
doFillHoles - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Flag to enable hole filling.
doGauss - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Preprocess cytoplasm channel by Gaussian smoothing.
doHS(MTBImageDouble) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression: Does the hysteresis thresholding.
doHysteresisThresholding - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression: Flag to enable/disable additional hysteresis thresholding.
doIsotropicCalcutations(boolean) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures: Set flag for isotropic calculations.
doIteration() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Here the main work should be done.
doIteration() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
doIteration() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy: Performs one single optimization step, i.e. iterates once over all points.
doIteration() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Performs one single optimization step.
domainXmax - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Maximal x coordinate of user-specified domain.
domainXmin - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Minimal x coordinate of user-specified domain.
domainYmax - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Maximal y coordinate of user-specified domain.
domainYmin - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Minimal y coordinate of user-specified domain.
doMorphOps - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Flag to enable/disable morphological pre-/postprocessing.
doNMS() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression: Applies non-maximum-suppression to the input data.
doNormalization - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE: do normalization?
doNucleiSeparation - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Flag to enable separation of merged nuclei regions.
doPCA - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Perform PCA in second stage?
doPCA() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Performs a Karhunen-Loeve transformation on the cluster distribution data.
doPCA - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Perform PCA in second stage?
doPCA() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Performs a Karhunen-Loeve transformation on the cluster distribution data.
doProtrusionIndentationAnalysis(MTBContour2DSet, Vector<double[]>, int, int) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper: Method to perform analysis of intrusions/protrusions along contours.
doRemoveSpines(boolean) - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor: Enable/disable removal of spines.
doResampleSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Returns true if snake should be resampled during optimization.
doResampling - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Flag to enable/disable snake resampling.
dotGlobalAttributes - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
dotGraphFilename - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
doUseSpecifiedDomain(boolean) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Enable/disable use of domain specified by the user.
draw(MTBXMLRootImageAnnotationType, MTBImage, Drawing.DrawType, EnumSet<Drawing.ROOTSEGMENT_STATUS>) - Static method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing
draw(Graphics) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI: Called method to temporary view the selected set of borders from the Roi-Manager into the current image.
draw(Graphics) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI: Called method to temporary view the selected set of contours from the Roi-Manager into the current image.
draw(Graphics) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI: Called method to temporary view the selected set of polygons from the Roi-Manager into the current image.
draw(Graphics) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI: Called method to temporary view the selected set of regions from the Roi-Manager into the current image.
draw(Point2D.Double[]) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
drawBordersToImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Draws result contours to an image.
drawCircle2D(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Draws a circle at the given position into the x-y-plane.
drawContour(MTBImage, Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Draw a contour into an image.
DrawContour2DSet - Class in de.unihalle.informatik.MiToBo.visualization.drawing: A class to visualize 2D contours.
DrawContour2DSet() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet: Default constructor.
DrawContour2DSet(MTBContour2DSet) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet: Simple constructor with contour set.
DrawContour2DSet(MTBContour2DSet, MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet: Constructor with contour set and image.
drawContours(MTBImage, MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Draw contours of resultImg and if non null initLabelImg into inIMg and return this result in a new image
DrawEllipse - Class in de.unihalle.informatik.MiToBo.visualization.drawing: Operator to draw an ellipse to a given image.
DrawEllipse() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Default constructor.
drawEllipse() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Draw ellipse to image.
drawFilledCircle(ImagePlus, int, int, float, int) - Static method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing: Draws a filled circle at position ('x', 'y') with radius 'radius'.
drawFilledCircle2D(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Draws a 2D circle at the given z position into the x-y-plane.
Drawing - Class in de.unihalle.informatik.MiToBo.apps.minirhizotron.utils: Created by Andreas Lange on 8/30/17.
Drawing() - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing
Drawing.DrawType - Enum in de.unihalle.informatik.MiToBo.apps.minirhizotron.utils
Drawing.ROOTSEGMENT_STATUS - Enum in de.unihalle.informatik.MiToBo.apps.minirhizotron.utils
DrawLine - Class in de.unihalle.informatik.MiToBo.visualization.drawing: Implementation of the Bresenham line drawing algorithm according to Wikipedia.
DrawLine() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
DrawLine(MTBImage, Point2D.Double, Point2D.Double) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
drawLine2D(Line2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Draws a 2D line into the neuron image.
drawLine2D(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Draws a 2D line into the current slice of the image.
drawLine2D(int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Draws a 2D line into the given slice of the image.
drawLine2D(Line2D.Double, Point2D.Double, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Draws a 2D line into the neuron image.
DrawMask2D - Class in de.unihalle.informatik.MiToBo.visualization.drawing: Operator for drawing a mask into an image.
DrawMask2D() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D: Default constructor.
DrawMask2D(MTBImage, MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D: Constructor.
drawPixels(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI: Called method to draw the selected entry from the Roi-Manager into the current image.
drawPixels(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI: Called method to draw the selected entry from the Roi-Manager into the current image.
drawPixels(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI: Called method to draw the selected entry from the Roi-Manager into the current image.
drawPixels(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI: Called method to draw the selected entry from the Roi-Manager into the current image.
drawPoint2D(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Draws a point at given position into the x-y-plane.
drawPolygon(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Draw a polygon into an image (in red color).
drawPolygon(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Draw a polygon into an image.
drawPolygon(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Draw snake into an image.
DrawPolygon2DSet - Class in de.unihalle.informatik.MiToBo.visualization.drawing: A class to visualize 2D polygons.
DrawPolygon2DSet() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet: Default constructor.
DrawPolygon2DSet(MTBPolygon2DSet) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet: Simple constructor with polygon set.
DrawPolygon2DSet(MTBPolygon2DSet, MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet: Constructor with polygon set and image.
drawPolygonPoints(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Draw polygon points into an image (in red color and as crosses).
drawPolygonPoints(MTBImage, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Draw polygon points into an image.
drawPolygonPoints(MTBImage, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Draw snake points into an image (as crosses).
DrawRegion2DSet - Class in de.unihalle.informatik.MiToBo.visualization.drawing: A class to visualize 2D regions.
DrawRegion2DSet() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Default constructor where no parameters are set.
DrawRegion2DSet(DrawRegion2DSet.DrawType, MTBRegion2DSet) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Simple constructor to create the most common region image types.
DrawRegion2DSet(DrawRegion2DSet.DrawType, MTBRegion2DSet, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Simple constructor to draw the most common region image types to a given image.
DrawRegion2DSet.DrawType - Enum in de.unihalle.informatik.MiToBo.visualization.drawing: Type of image to be drawn.
drawRegionIDsToOutputImages - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Flag to enable/disable drawing region IDs.
drawRegions(MTBRegion2DSet, int, int, int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing: draw regions to the output image
drawRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
drawResultsToImage(MTBImageRGB, Lines, Junctions, boolean, boolean) - Static method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Draw results to given image.
drawRootIDs(MTBXMLRootType[], MTBImage, Color) - Static method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
drawSample(int, T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.IndependentSamplingDistribution: Generate a new sample from this density by drawing only one independent variable for a given realization x.
drawSample() - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.SamplingDistribution: Generate a new sample from this density.
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
drawSample(int, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistributionIndep
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistributionIndep
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
drawSample(int, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
drawSample(int, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
drawSampleDebug(DataAssociation, OutputStream) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
drawSampleDebug(DataAssociation, OutputStream) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
drawSampleDebug(DataAssociation, OutputStream) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
drawSegment(ImagePlus, int, int, int, int, int, int, int) - Static method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing: Draws a filled rectangle.
drawSpot(MTBImage, MTBRegion2D, int, int, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D: Draw region to an image at time=t and channel=c with specified color.
drawSpots - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
drawSqare(MTBImage, MTBRegion2D, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D: Draw square to an image at time=t and channel=c with specified color and size=2*radius+1.
drawStringToImage(MTBImageRGB, String, int, int, int, int, int) - Static method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Draws string at given position into image.
drawStringToImage(MTBImageShort, String, int, int, int) - Static method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Draws string at given position into image.
drawStringToImage(MTBImage, String, int, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Draws string at given position into image.
DrawStringToImage - Class in de.unihalle.informatik.MiToBo.visualization.drawing: Operator to draw a given string into a given image.
DrawStringToImage() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage: Default constructor.
DrawTracks2D - Class in de.unihalle.informatik.MiToBo.visualization.drawing: Draw trajectories of tracked observations over time.
DrawTracks2D() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D: Constructor.
drawTrajectories - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
drawTrajectories(Matrix, Matrix, int, int, int, MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D: Draw trajectory between two points at the given and all later timepoints until t_last
DrawType() - Constructor for enum de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing.DrawType
drawType - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Type of image to be created.
DrawType() - Constructor for enum de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet.DrawType
duplicate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Duplicates the object.
duplicate(ALDOperator.HidingMode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Duplicates the object.
duplicate(MTBOperator) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Deprecated.
duplicate(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
duplicate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
duplicateImageJType(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
duplicateNonImageJType(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
DynamicColorLUT - Class in de.unihalle.informatik.MiToBo.visualization.drawing: A color lookup table that generates colors dynamically and randomly for indices that do not exist.
DynamicColorLUT() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT: Constructor with a (seeded) random generator and channel offset = 20.
DynamicColorLUT(Random) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT: Constructor for a specific random generator and channel offset = 20..
DynamicColorLUT(Random, int) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT: Constructor for a specific random generator and a given channel offset

E

e - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Implicit curve parameter e.
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Return the complete energy for the level set function phi.
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
E(int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE: Get energy term a pixel (x,y) for phi. 2D only
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
E(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE: Get energy term a voxel (x,y,z) for phi.
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
e_x - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE: x coordinate of displacement vector defining neighbor hood
e_y - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE: x coordinate of displacement vector defining neighbor hood
eccentricities - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
eccentricities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
edgeData - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Data of the MTBGraphEdge, included in a vector object.
edges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Vector of included graph edges.
eigenVals - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Set of computed eigenvalues.
eigenVects - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Matrix of eigenvectors, each column containing a vector.
eightconnected - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
eightconnected - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Use 8-connectedness in component labeling (only active if ConvexHullExtraction.inType is InputType.IMAGE).
elemCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Get a border by index.
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Get a contour by index.
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: Get a specific line segment by index including a safety check.
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Get a polygon by index.
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Get a region by index
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Get a region by index
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Get a region by index
elementMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Matrix for elements markers: 0 = no mark, 1 = starred, 2 = primed
ellipse - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Ellipse to draw.
ellipseDistThresh - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Ellipse distance threshold.
ellipseDistThresh - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules: Maximal distance between contact points along ellipse contour.
ellipsoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Function to extract elliptical snake primers.
enableComponent() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
enableComponent() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
enableComponent() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.
enableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
enableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Enables graphical elements to allow for value changes.
enableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
enableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Reactivates the configuration window to allow for value changes.
enableEnergyCalculation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Enable energy calculation in each iteration.
enableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D: Enable kernel normalization.
enableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D: Enable kernel normalization.
enableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Enable kernel normalization.
enableSaveIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Save intermediate results.
enableSaveIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Activates writing of intermediate results to disc.
enableShowIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Enable display of intermediate results.
enableShowIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Activates display of intermediate results.
end - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
endPoint - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: End pixel of the path.
endPointHash - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
endPosOnContour - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Index of segment end pixel on contour.
energies - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: List of snake energies.
energies - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
energies - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
energy - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
energy - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
energy - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
energy - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Current energy of the snake.
energyCalculationRequested - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Flag for invoking energy calculations.
energyConfWins - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Mapping of short names to configuration windows.
energyConfWins - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Mapping of short names to configuration windows.
energyData - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
energyLabel - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Label of available external snake energies, which are usable by the detector.
EnergyNormalizationMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.EnergyNormalizationMode
energyPotential - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D: Potential field reconstructed from GVF.
energyRange - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Interval boundaries of adapted energy interval.
energySelection - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Combobox for selecting energies.
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives: Set of energies to apply.
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Set of energies.
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: List of snake energies to be used in segmentation.
energySetFields - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline: Fields of a EnergySet we parse
energyTab - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: List of selected energies.
energyTab - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: List of selected energies.
energyTabModel - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Model for the energy table.
energyTabModel - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Model for the energy table.
energyWeights - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Individual energy weights.
energyWeights - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Individual energy weights.
energyWeightsNormed - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy: List of normalized energy weights.
energyWeightsNormed - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: List of normalized energy weights.
enhanceBoundaries(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Enhance cell boundaries by applying a vesselness enhancement filter.
enhanceR - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Niblack factor R.
entireTargetIDs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: The targetIDs of all targets that have ever existed up to current time
entriespanel - Variable in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel: panel to hold all the entries
entropyFiltering(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
entropyFilterSize - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
entropyFilterSize - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
entropyFilterSize - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
entropyImg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
ep - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine: End point of segment.
epsilon - Static variable in class de.unihalle.informatik.MiToBo.core.datatypes.defines.MTBConstants: Accuracy for numerical calculations.
epsilon - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper: Epsilon value to configure scale to use.
epsilon - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives: Epsilon value for approximation of Heaviside function.
equalizeImageHisto(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization: Apply histogram equalization to the given image.
equals(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Test if this object and img are of same type, have same size and same values
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D.IntersectionPoint2D: Checks if two intersection points are equal.
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
equals(MTBLevelsetFunctionPDE) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: are these two LevelSets equal?
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
equalSize(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Test if this object and img have the same size in x-, y-, z-, t- and c-dimension
equalWeights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
equalWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Returns true if all particle weights are equal
equatorLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Length of the equator in pixels.
EraseLargeComponents(MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Function to remove large components from a binary image.
eraseNonCompactComponents(MTBImageByte, double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Function to remove all non compact/circular components of a binary image.
EraseRoundComponents(MTBImageByte, double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Remove components with small eccentricity.
EraseSmallComponents(MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Function to remove small components from a binary image.
erode(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
erode1D(double[], int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
erodeComponent(int, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: erode one component with given label
erodeImageWithCircle(MTBImage, int) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Erode an image of type MTBImageByte.
erodeSize - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
erodeSize - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: The size of the structuring element for erosion to compute seed regions.
erodeSize - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: The size of the structuring element for erosion to compute seed regions.
error - Variable in exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DException
error - Variable in exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2DException
error - Variable in exception de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2DException
error - Variable in exception de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphException
error - Variable in exception de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DException: Exception error message.
error_msg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
essPercentage - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
esspercentage - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
estimateMean(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Suche nach bestem Mittelpunkt des Embryos: ueberpruefe kreisfoermige Raster (8 Punkte +Mittelpunkt des Bildes) um Bildmittelpunkt aus Kriterium: max. min.
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Estimate internal parameters (if any) for the level set function phi assumed to be associated with this energy object.
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
estimateWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: If true the widths of the lines are estimated.
euklidDist(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Hilfsmethode zur Bestimmung der euklidischen Distanz zw. 2 Punkten
evalData - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Result data.
evalData - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.MTBGroundtruthEvaluationData: Result data object.
evaltime - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult: time that elapsed for evaluation
EvalTracks - Class in cmdTools.tracking.multitarget: Commandline tools to compare observation-files, i.e. the target-IDs of the individual observation, to evaluate the quality of target-association in one file with respect to the other that is interpreted as groundtruth.
EvalTracks() - Constructor for class cmdTools.tracking.multitarget.EvalTracks
EvaluatableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for distributions that can be evaluated for each realization x of its random variable X.
evaluateFunction(double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.DistanceTargetFunction
evaluateFunction(double[]) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
evaluateGradientOfFunction(double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.DistanceTargetFunction
evaluateGradientOfFunction(double[]) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
EvaluationMeasure - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures: Base class for evaluation measures comparing a segmentation result against a groundtruth segmentation.
EvaluationMeasure(MTBImageShort, MTBImageShort) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Constructor.
EvaluationMeasure() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Default constructor.
EvaluationMeasureContours - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures: Class implements the super class for contour detection evaluation operators.
EvaluationMeasureContours() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours: Default constructor.
examineDataset() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Extracts number of samples and their dimension from dataset.
ExceptionType() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException.ExceptionType
exclude - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
excludeBackground - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage: If true all background pixels, defined as pixels with label equals backgroundLabel are excluded
excludeBorderRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing: exclude regions that are adjacent to the image borders
excluded - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
excludeLargeRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing: exclude regions that are larger than the predefined (Parameter maxArea) maximum
excludeList - Variable in class de.unihalle.informatik.MiToBo.clustering.KMeans: Exclude list with indices of attributes to ignore.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Optional mask to exclude particles in certain regions.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Optional mask to exclude particles in certain regions.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Global exclude mask for image to be segmented.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Mask to exclude image pixels from calculations.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
excludeParticlesInNuclei - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Flag to ignore particle in nuclei regions.
excludeSmallRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing: exclude regions that are smaller than the predefined (Parameter minArea) minimum
executeOperator(ALDOperatorLocation) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
existingTargetIDs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: The targetIDs of the existing target at the specific time
expectedWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Expected width of vessels.
ExponentialDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl: Exponential distribution.
ExponentialDistribution(double) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution: Constructor for exponential distribution lambda*exp(-lambda*x) if x >= 0.
ext - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
extendLine - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: If true lines are extended.
extensions - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
extract(File[], double) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer: segment the given images and extract their features for classification
extract(Vector<File>, double) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer: segment the given images and extract their features for classification
extractBorders() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Extract requested borders for given input data.
extractCentroids() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D: extract centroids from labeled regions
extractCentroids(MTBImage, boolean, double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
extractedNeurites - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
extractFeatures() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal: Method to extract code histogram from the given image.
extractHullsOnRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
extractLabelsSizesOverlaps() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Extracts evaluation data in terms of overlaps and missed pixels.
extractLocalComponents() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Extracts list of connected components from Otsu thresholded input image.
extractMolProf(MTBImage, MTBNeurite2DSet, String, String) - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Extraction of molecular profiles along the detected neurites.
extractMSERs(Img<T>) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Method to calculate MSERs from given image.
extractParticles - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
extractParticles(MTBImage, MTBNeurite2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Extraction of molecular particles along the detected neurites.
extractPointVectorPolygon(MTBXMLPolygon2DType) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Extract the list of polygon points for a polygon.
extractPointVectorSnake(MTBXMLPolygon2DType) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Extract the list of polygon points for a snake.
extractPrecursorInfos - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Flag to enable/disable extraction of precursor infos.
extractProfiles - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
extractRegionBorders() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves: Extract borders of detected ellipses.
extractRegionBorders() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Extract borders of detected regions.
extractTrajectoriesWithOffsets() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer: extract Hashtables containing the centroid locations of each trajectory
and the offsets for the starting time of each trajectory

F

f - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Implicit curve parameter f.
F - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians: state-transition matrix
factor - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
factorial(int) - Static method in class de.unihalle.informatik.MiToBo.math.MathX: Calculates the factorial of the given natural number.
factorialVals - Static variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Pre-computed factorial values.
factory - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState: factory that holds information how a target's state is composed
FactoryMethod() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.FactoryMethod
factoryMethod - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
factoryX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
factoryX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution: multi state factory for condition variable, used for validity checks
factoryX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution: multi state factory for condition variable, used for validity checks
factoryZ - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
factoryZ - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution: multi state factory for observation variable, used for validity checks
falseFileNames - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
falseNegativeFileNames - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
falsePositiveFileNames - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
featureCalcResults - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult: Tile-wise result data of the different calculators.
FeatureCalculator - Class in de.unihalle.informatik.MiToBo.features: Super class for operators calculating features on images.
FeatureCalculator() - Constructor for class de.unihalle.informatik.MiToBo.features.FeatureCalculator: Default constructor.
FeatureCalculatorHaralickMeasures - Class in de.unihalle.informatik.MiToBo.features.texture: Calculates set of Haralick co-occurrence texture features from an image.
FeatureCalculatorHaralickMeasures() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures: Default constructor.
FeatureCalculatorHaralickMeasures.HaralickDirection - Enum in de.unihalle.informatik.MiToBo.features.texture: Directions available for matrix calculations.
FeatureCalculatorHaralickMeasuresResult - Class in de.unihalle.informatik.MiToBo.features.texture: Class representing the result of statistical feature calculations.
FeatureCalculatorHaralickMeasuresResult(double[]) - Constructor for class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult: Default constructor.
FeatureCalculatorIntensityStats - Class in de.unihalle.informatik.MiToBo.features.statistical: Calculates statistical features on images tile-wise, based on FeatureCalculator.
FeatureCalculatorIntensityStats() - Constructor for class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats: Default constructor.
FeatureCalculatorIntensityStatsResult - Class in de.unihalle.informatik.MiToBo.features.statistical: Class representing the result of statistical feature calculations.
FeatureCalculatorIntensityStatsResult(ImageStatistics.StatValue, double) - Constructor for class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult: Default constructor.
FeatureCalculatorLBP - Class in de.unihalle.informatik.MiToBo.features.texture.lbp: Implements an extended version of local binary patterns (LBPs).
FeatureCalculatorLBP() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBP: Default constructor.
FeatureCalculatorLBPJFeatureLib - Class in de.unihalle.informatik.MiToBo.features.texture.lbp: Abstract super class for LBP operators building on the JFeatureLib.
FeatureCalculatorLBPJFeatureLib() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Default constructor.
FeatureCalculatorLBPJFeatureLib.FeatureType - Enum in de.unihalle.informatik.MiToBo.features.texture.lbp: Type of feature to be extracted.
FeatureCalculatorLBPOriginal - Class in de.unihalle.informatik.MiToBo.features.texture.lbp: Operator for extracting Local Binary Patterns (LBPs).
FeatureCalculatorLBPOriginal() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal: Default constructor.
FeatureCalculatorLBPOriginal.NeighborhoodSelection - Enum in de.unihalle.informatik.MiToBo.features.texture.lbp: Kind of neighborhood to be considered for code calculation.
FeatureCalculatorLBPResult - Class in de.unihalle.informatik.MiToBo.features.texture.lbp: Class representing the LBP features.
FeatureCalculatorLBPResult(double[]) - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult: Default constructor.
FeatureCalculatorLBPRIU - Class in de.unihalle.informatik.MiToBo.features.texture.lbp: Implements rotation invariant uniform local binary patterns (LBP-RIU).
FeatureCalculatorLBPRIU() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIU: Default constructor.
FeatureCalculatorLBPRIULUTs - Class in de.unihalle.informatik.MiToBo.features.texture.lbp: Class keeping look-up tables for rotation invariant LBP codes.
FeatureCalculatorLBPRIULUTs() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs
FeatureCalculatorResult - Interface in de.unihalle.informatik.MiToBo.features: Interface for result data returned from classes extending FeatureCalculator.
FeatureColorMapper - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology: This operator maps numerical feature values to objects in an indexed image.
FeatureColorMapper() - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper: Default constructor.
featureDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Feature directory.
featureExtractor - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Feature extractor to apply.
featureExtractor - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Feature extractor to apply.
featureLines - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Borderlines that separate the neurite from the soma and additionally separate the neurite from its growth cone.
featureNameMapper - Static variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
FeatureNames() - Constructor for enum de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D.FeatureNames
FeatureNames() - Constructor for enum de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer.FeatureNames
featureOps - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: List of feature calculators to apply.
featureParameters - Static variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: List of parameters relevant for feature extraction phase.
featurePoints - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Vector of detected feature points for each neurite.
featurePoints - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Features of the single neurite branches.
FeatureType() - Constructor for enum de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib.FeatureType
fg_value - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
fgValue - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
field - Variable in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder: Vector field the potential is reconstructed for.
fieldMap - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline: used to work around generics
FieldOperation() - Constructor for enum de.unihalle.informatik.MiToBo.fields.FieldOperations2D.FieldOperation
FieldOperations2D - Class in de.unihalle.informatik.MiToBo.fields: Class implements several operations on a 2D vector field.
FieldOperations2D() - Constructor for class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Standard constructor.
FieldOperations2D(MTBVectorField2D, MTBImageDouble, FieldOperations2D.FieldOperation) - Constructor for class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Constructor to create a new field operation operator.
FieldOperations2D(MTBVectorField2D, FieldOperations2D.FieldOperation) - Constructor for class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Constructor to create a new field operation operator.
FieldOperations2D.FieldOperation - Enum in de.unihalle.informatik.MiToBo.fields: Several operation types on a 2D vector field.
fieldSizeX - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Vector field size in x-direction.
fieldSizeY - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Vector field size in y-direction.
file - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker: File name for optionally saving the image.
file_name_noExtension - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Current image name without file extension.
fileName - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: File name of the current multichannel fluorescence image.
fileName - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Name of input image file.
filename - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
fileName - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
fileName - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
fileName - Variable in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
FilenameGenerator - Class in de.unihalle.informatik.MiToBo.tools: Utility operator to generate a filename from a given filename.
FilenameGenerator() - Constructor for class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
fileNameOut - Variable in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
FileOptionsRefresher(ImageReaderOptionsPane, File[]) - Constructor for class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane.FileOptionsRefresher
filePath - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Textfile with mapping.
FilePathManipulator - Class in de.unihalle.informatik.MiToBo.io.tools: Class providing helpers to manipulate file and directory paths.
FilePathManipulator() - Constructor for class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator
files - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane.FileOptionsRefresher
files - Variable in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData: List of files (no subdirectories!)
fileSep - Static variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: File separator character, operating system dependent.
fill(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
fill(MTBImage, Color) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
fillBlack() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set all pixels of the image to black, i.e. the minimal available value.
fillHoles(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
FillHoles2D - Class in de.unihalle.informatik.MiToBo.segmentation.regions.filling: Operator to fill holes in connected components of binary or label images.
FillHoles2D() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: Default constructor.
FillHoles2D(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: Constructor with input image.
fillImage(MTBImage, double, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools: Fill the specified image with a gray value.
fillImage(MTBImage, Color, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools: Fill the image with a RGB color value.
fillPanel(String[], boolean[]) - Method in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel: Adds checkboxes to the panel according the entries array.
fillPanel(String[], String) - Method in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel: Adds radio buttons to the panel according the choices array.
fillPanel(HashMap<String, Component>) - Method in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel: Add the components in the HashMap to the panel.
fillResultTable(HashMap<String, HashMap<Integer, Double>>) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Method to fill the result table.
fillWhite() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set all pixels of the image to white, i.e. the maximal available value.
fillWhite() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
filter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample: The current state distribution of targets in this sample estimated by a prediction filter
filterImage - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
filterMethod - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
FilterMethod() - Constructor for enum de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter.FilterMethod
filterMode - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
FilterMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D.FilterMode
filterRegions(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Checks region sizes and average intensities against specified intervals.
filterValidCellRegions(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Postprocesses cell regions and applies some filtering.
findEndpointBranches(MTBImageByte) - Static method in class de.unihalle.informatik.MiToBo.morphology.BinaryImageEndpointTools: Extracts set of endpoint branches from a given binary image.
findEndpoints(MTBImageByte) - Static method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Detect end-points in binary image.
findEndpoints(MTBImageByte) - Static method in class de.unihalle.informatik.MiToBo.morphology.BinaryImageEndpointTools: Extracts set of endpoints from a given binary image.
findMiddleScale(double, double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Numerically finds the middle scale between to given scales.
findNextPoint(Point2D.Double, int, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Find direction to next pixel in specific direction from the last pixel.
findPrefixes(Vector<String>) - Static method in class de.unihalle.informatik.MiToBo.tools.strings.StringAnalysis: Helper to recursively extract common prefixes.
finished - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Flag to indicate if operations are finished.
firstOneImageOneConstOrdinal - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
firstOneImageOnlyOrdinal - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
FirstOrderMoment<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for classes that provide a first order moment.
FitEllipseToPointSet - Class in de.unihalle.informatik.MiToBo.math.fitting: Operator that fits an ellipse to a given set of 2D points.
FitEllipseToPointSet() - Constructor for class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet: Default constructor.
FitQuadraticCurveToPointSet - Class in de.unihalle.informatik.MiToBo.math.fitting: Operator that fits a quadratic curve or conic to a given set of 2D points.
FitQuadraticCurveToPointSet() - Constructor for class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet: Default constructor.
fittingEnergy - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
five_thirds - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
FLAG_LENGTH - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE: Bit mask for length energies for debugging purposes.
FLAG_SOLVER - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
FLAG_SOLVER2 - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
FluorescentCellSegmenter - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D: This operator is for segmenting images or image sequences containing fluorescently labeled cells
FluorescentCellSegmenter() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
FluorescentCellSegmenter(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
fn - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
fn - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc: False negatives.
FNclutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
FNtrackend - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
FNtracksegment - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
FNtrackstart - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
foreground - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Foreground color of the foreground object.
ForegroundColor() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.ForegroundColor
foregroundToBackground(Vector<Point2D.Double>, MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Set the pixel value containing in a java.util.Vector of java.awt.geom.Points2D to 0.
format - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Target format.
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtColorDataIOCmdline: Converts an java.awt.Color object to a string-representation in the format "rINT:bINT:gINT:aINT".
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtPoint2dDataIOCmdline: Converts an java.awt.geom.Point2D.Double object to a string-representation in the format (x;y).
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBWrapperDataIOCmdline: Format the given object value to a string
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.RandomGeneratorDataIOCmdline: Get a string representing the seed of the specified Random generator.
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
forwardDifferencing_X(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
forwardDifferencing_Y(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
forwardDifferencing_Z(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
fp - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
fp - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc: False negatives.
FPclutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
fps - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
fps - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
fpsfield - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
FPtrackend - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
FPtracksegment - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
FPtrackstart - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
fracDigits - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
fracDigits - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
frameHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Fixed height of window.
frameHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Fixed height of window.
frameHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Fixed height of window.
frameWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Fixed width of window.
frameWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Fixed width of window.
frameWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Fixed width of window.
frequency - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Filter frequency.
fromMaxVal - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
fromMinVal - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
fromXMLType(MTBXMLMatrixType) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter: Obtain a JAMA matrix from its xml-beans type
fromXMLType(MTBXMLMultiStateMMIDType) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter: Obtain a MultiState object from its xml-beans representation
fromXMLType(MTBXMLMultiStateMMIDVectorType) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter: Obtain a Vector> object from its xml-beans representation

G

GaborFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic: 2D Gabor filter.
GaborFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Default constructor.
GaborFilter2D.KernelPart - Enum in de.unihalle.informatik.MiToBo.filters.linear.anisotropic: Allows to request kernel masks for real and complex parts independently.
GaborFilter2D.ResultType - Enum in de.unihalle.informatik.MiToBo.filters.linear.anisotropic: Reponse mode.
gamma - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
gamma - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Step-size in iterative snake optimization.
gamma - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
gamma - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
gamma - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
gammaAdaptive - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Vector containing the current gamma values (step sizes).
GammaCorrection2D - Class in de.unihalle.informatik.MiToBo.enhance: Gamma correction on a 8- oder 16-bit image for one- or multi-channel images.
GammaCorrection2D() - Constructor for class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Standard constructor.
GammaCorrection2D(MTBImage, Double, Integer) - Constructor for class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Constructor to create a new gamma correction 2D operator.
GammaCorrection2D(MTBImage, Integer) - Constructor for class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: No gamma value is set.
gammaUpdater - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Gamma update strategy.
GapCloseMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.GapCloseMode
gapMode - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Mode for closing gaps.
gauss2poisson(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Transforms image with gaussian noise to image with poisson noise J.
GaussFilter - Class in de.unihalle.informatik.MiToBo.filters.linear: Multidimensional Gauss filter class.
GaussFilter() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Constructor with default parameters sigmaX=1, sigmaY=1, sigmaZ=0, sigmaT=0, sigmaC=0, kernelTruncation=3, sigmaInterpretation=PHYSICALSIZE.
GaussFilter(MTBImage, double, double) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Constructor for Gaussian filtering in x- and y-dimension.
GaussFilter(MTBImage, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Constructor for Gaussian filtering in x-, y- and z-dimension.
GaussFilter(MTBImage, double, double, double, double, double, MTBImageWindow.BoundaryPadding, double, GaussFilter.SigmaInterpretation) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Constructor for Gaussian filtering.
gaussFilter() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: compute the Gaussian filter
GaussFilter.SigmaInterpretation - Enum in de.unihalle.informatik.MiToBo.filters.linear: Indicator how to interpret the specified standard deviations: - PIXEL: Sigma is given in pixels - PHYSICALSIZE: Sigma is given in terms of the physical pixel size (see MTBImage.getStepsizeX/Y/Z/T, in c-dimension always pixel interpretation is used)
GaussFilterDouble1D - Class in de.unihalle.informatik.MiToBo.math.arrays.filter: This class implements a Gaussian filter for 1D arrays.
GaussFilterDouble1D() - Constructor for class de.unihalle.informatik.MiToBo.math.arrays.filter.GaussFilterDouble1D: Default constructor.
gaussFilterImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Gauss filtered input image (for internal use only).
gaussian - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians: multivariate gaussian density object for evaluation
gaussian - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians: multivariate gaussian density object for evaluation
GaussianDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl: A multivariate Gaussian distribution.
GaussianDistribution(int) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution: Constructor for a Gaussian distribution of dimension DOF with the zero vector as mean, the unity matrix as covariance matrix and a new random generator for sampling
GaussianDistribution(int, Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution: Constructor for a Gaussian distribution of dimension DOF with the zero vector as mean, the unity matrix as covariance matrix and a given random generator for sampling
GaussianDistribution(Matrix, Matrix) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution: Gaussian distribution with given mean, covariance and a new random generator for sampling
GaussianDistribution(Matrix, Matrix, Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution: Gaussian distribution with given mean, covariance and random generator for sampling
gaussians - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
gaussianSigma - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Standard deviation of Gaussian kernel in curvature smoothing.
GaussMixDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl: A multivariate Gaussian mixture distribution.
GaussMixDistribution(GaussianDistribution[], Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution: Constructor with equally weighted Gaussian components
GaussMixDistribution(GaussianDistribution[], double[], Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution: Constructor for weighted Gaussian components
gaussmixtures - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
gaussnoise - Variable in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
GaussPDxFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic: 2D linear filter implementing first partial derivative of a Gaussian in x.
GaussPDxFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D: Default constructor.
GaussPDxxFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic: 2D filter implementing second partial derivative of Gaussian in x.
GaussPDxxFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Default constructor.
gaussSigma - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Sigma for Gaussian smoothing.
gaussStdDev - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D: Standard deviation of the Gaussian.
gaussStdDev - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D: Standard deviation of the Gaussian.
gaussStdDev - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Standard deviation of the Gaussian.
gaussStdDevX - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Standard deviation of the Gaussian in x.
gaussStdDevY - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Standard deviation of the Gaussian in x.
generateCoarseSoma() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Compute a coarse neuron cell body region (soma).
generateHelpMenu() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
generateHelpMenu() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
generateHelpMenu() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
generateHelpMenu() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Set up the help menu.
generateNeuriteRegions(Vector<Vector<Vector<Line2D.Double>>>, Vector<Vector<Vector<Point2D.Double>>>) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Generate neurite region from calculated features.
generateNextStates(MultiState<MotionModelID>, LinearTransformGaussNoise[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
generateObservations(MultiState<MotionModelID>, LinearTransformGaussNoise, MultiStateFactory<MotionModelID>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
generateSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Generates segmentation objects given specified data.
generateSkelGraph() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Compute the skeleton graph for the complete neuron region.
generateStackWithIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Generates a stack with intermediate results.
generateStructuringElement() - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
GeneratorInfo() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
GenericDiscreteDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl: A generic discrete distribution
GenericDiscreteDistribution(double[], Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution: Constructor.
GenericDiscreteDistribution(double[], Random, boolean) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution: Constructor.
genInfo - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: Get a specific line segment by index.
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Get a region by index
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Get a region by index
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Get a region by index
get(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Get the function value at position (x,y,z).
get(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: get the value of this function at the position of the predecessor of ( x, y, z )
get2DInterface(MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Generates 2D segmentation.
get2DMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Generates a synthetic 2D mask according to given specification.
get3DInterface(MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Generates 3D segmentation.
get3DMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Generates a synthetic 3D mask according to given specification.
get3SigClippedStdDev(MTBImage) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Get the standard deviation (sigma) of an image only using values clipped by 3*sigma from a first estimate of sigma
get8NeighborsPhase(int, int, short[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Compute phases of 8 neighbors of (x,y) and store these in the array nb.
getActivityArray() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult: Get reference to activity array.
getActivityArray() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Returns current activity array.
getActualSliceOnly() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Get flag for thresholding only the actual slice (true) or the whole image (false)
getAlgorithm() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
getAllEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Get all edges of the node.
getAllInner() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Get all inner contours from the contour object.
getAllInnerBorders() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Get all inner borders from the border object.
getAllInputImages() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Getter for all input images.
getAllInputTreelines() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Getter for the input treelines of the specified layer.
getAllNodesDepthFirst() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree: Get all nodes in a depth-first sorting.
getAllPaths(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get the pixels of all paths of the neurite skeleton graph.
getAllPixels(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get all pixels of the neurite skeleton graph from the nodes and edges.
getAllPixels(Vector<Point2D.Double>, MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get all pixels of the neurite skeleton graph from the nodes and edges.
getAllResultTreelines() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Getter for all result treelines.
getAllSubtreeNodesDepthFirst() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: Recursively collect all nodes of the subtree below this node.
getAllTiles() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Generates and returns array of all tiles.
getAlpha() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get snake length term weight alpha.
getAlpha() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get weighting factor for snake length term.
getAlphaDecrease() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix: Get the fix alpha decrease value.
getAnalysisImage() - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Get image with visualized analysis results.
getAnalyzedImages() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get vector of analyzed images.
getApicalLength() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Get apical length.
getAPIText() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorDocumentationFrame
getAPIURL() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorDocumentationFrame
getApplicationMode() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D: Get application mode.
getArea() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Return the area of the region in pixels.
getArea() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
getArea() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape: Get area of the shape.
getArea() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeCurve
getArea() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine
getArea() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapePolygon
getArea() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeRegion
getAreaFracMatrix(MTBRegion2DSet, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
getAreaFraction(MTBRegion2D, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
getAreaFraction() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff: Get area fraction.
getAreaFraction() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset: Get area fraction.
getAreaFractions(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
getArithmeticOperation() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
getAssociatedObservations(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
getAssociatedObservations(int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation: Get the indices of all observations that are associated with the specified state.
getAssociatedTargets(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
getAssociatedTargets(int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation: Get the indices of all targets that are associated with the specified observation.
getAvailableCodecs() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Return available codecs for movie writers (see Bio-Formats package loci.formats.out.QTWriter) represented by a hashmap.
getAvailableCompression() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Get the available compression methods for the specified file format.
getAvailableQualities() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Return available qualities for quicktime movie writers (see Bio-Formats package loci.formats.out.QTWriter) represented by a hashmap.
getAverageIntensities() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Get average intensities of regions.
getAverageMean(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
getAverageStdDev(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
getAvgConeWidths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get average widths of each neurite growth cone.
getAvgIntensity() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape: Get average intensity.
getAvgNeuriteWidths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get average widths of each complete neurite branch.
getAvgShaftWidths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get average widths of each neurite shaft.
getBackground(MTBImage, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelAreasToRegions
getBasalLength() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Get basal length.
getBaselineLength() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Get baseline length.
getBeta() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get snake curvature term weight beta.
getBeta() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get weighting factor for snake curvature term.
getBetaDecrease() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix: Get the fix beta decrease value.
getBGValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Get background value
getBhattacharyyaCoefficient(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
getBinaryImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get the image for binary mode.
getBinaryMask(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Generates binary mask for inside part of the polygon.
getBinaryMask(int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Generates binary mask for inside part of the polygon.
getBinaryMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Get a binary mask of the represented segmentation.
getBinaryMask(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Generates binary mask for inside part of the snake.
getBinaryMask(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Generates binary mask for inside part of the snake.
getBinaryPattern(int, int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapterRIU
getBinaryResultMap() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Returns the final binary map.
getBinIndex(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: determines the index of the histogram bin, to which a value is assigned, if histogram value range and binning were specified at creation
getBinMidpoint(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: determines the value midpoint of a histogram bin for given bin index, if
histogram value range and binning were specified at creation
getBinValue(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
getBorder() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Method to get the border object from the current 2D region, for example to visualize the regions.
getBorderCount() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult: Get number of borders in set.
getBorderLine(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Get borderlines between soma/neurite shaft and neurite shaft/growth cone.
getBorders() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult: Get set of region borders.
getBorderSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI: Get 2D border set from Roi.
getBorderSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Reads a ROI manager selection into a set of borders.
getBoundaryPadding() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get value of Parameter argument boundaryPadding.
getBoundaryPadding() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Get value of Parameter argument boundaryPadding.
getBoundaryPadding() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get value of Parameter argument boundaryPadding.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Calculates the axes-parallel bounding box of the contour.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Calculates the axes-parallel bounding box of the snake.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Calculates the axes-parallel bounding box of the region.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Calculates the axes-parallel bounding box of the region.
getBrancheCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get number of neurite branches.
getBranchLengths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get lengths of neurite branches along the complete neurite skeleton graph.
getBranchNodes() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get all branch nodes of the MTBNeuriteSkelGraph.
getBthImage() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Get black top-hat image.
getBthMaskSize() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Get mask size of black top-hat.
getC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getCalibration() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
getCalibration() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
getCalibration() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
getCalibration() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the calibration object.
getCalibration() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
getCalibration() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
getCandidates() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Returns set of detected candidate peaks.
getCConditionalProb(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: Get the probability of the associations at time t conditional on the previous associations and all observations up to time t.
getCellAvgSize() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Returns average size of detected cells.
getCellCount() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Returns number of detected cells.
getCellSizes() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Returns sizes of snake interiors.
getCenterOfMass_X() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Return x-coordinate of the center of mass.
getCenterOfMass_Y() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Return y-coordinate of the center of mass.
getCenterX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Get coordinate of center in x.
getCenterX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
getCenterY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Get coordinate of center in y.
getCenterY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
getCentralMoment(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Calculate central moment of the region of order p,q.
getCentralMoment(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
getCentre() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Return the center of the region as 3D point.
getCentreX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Return the x-coordinate of the center of the region.
getCentreY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Return the y-coordinate of the center of the region.
getCentreZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Return the z-coordinate of the center of the region.
getCentroid(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: auxiliary method to determine the centroid (x,y) and width/heigth of compoment with label in a double array of length 4 (should go in class/record)
getChaincode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Calculates chaincode from the outer contour.
getChannel() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Get the image channel.
getChannelB() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get a reference to the blue channel image.
getChannelG() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get a reference to the green channel image.
getChannelR() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get a reference to the red channel image.
getChannelsAreRGBFlag() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter: Get flag if RGB color channels are interpreted as real image channels.
getChart() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Get reference to resulting chart.
getChart() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Get reference to resulting chart.
getChartObject() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton: Returns the chart object associated with the button.
getChartShowButton() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowPanel: Returns the button object associated with the panel.
getChildNodes(Element) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
getChilds() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: Returns Vector with child nodes.
getChosenColor() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: Read currently selected color.
getCircularity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Calculates circularity of given region.
getCJointProb() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: Get the joint probability of all associations up to 'current time' (see getCurrentTime) conditional on all observations up to that time.
getClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
getClass(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
getClass(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
getClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
getClass(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Returns the class label of position (x,y).
getClass(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Returns the class label of position (x,y,z).
getClass(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
getClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
getClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
getClass(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
getClickedPoints() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame: Get a reference to the list of clicked points.
getCLogConditionalProb(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: Get the log of probability of the associations at time t conditional on the previous associations and all observations up to time t.
getCLogJointProb() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: Get the natural log of joint probability of all associations up to 'current time' (see getCurrentTime) conditional on all observations up to that time.
getClosestObjectPixelMap() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Get the calculated map of closest object pixels.
getClosestPointOnEllipse(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Returns the point on ellipse closest to given point.
getCodec() - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane: Get codec option
getCodec() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Get the codec (quicktime only)
getCodeDistributionRI(int) - Static method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs: Get array with LBP-RI code distributions.
getColor() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Get color of markers.
getColor() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Get the uniform color of the regions in a color image (COLOR_IMAGE only).
getColor(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT: Get the color for a given key.
getColorImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Get image of randomly colored regions, if the create-color-image-flag was set to true.
getColorList() - Method in class de.unihalle.informatik.MiToBo.color.tools.DistinctColorListGenerator: Returns color list.
getColumnCount() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
getColumnIDs() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputData: Returns index of currently selected column(s).
getColumnName(int) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
getCompactness() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: calculates compactness value according to
Carlos Martinez-Ortiz. "2D and 3D Shape Descriptors".
getCompactnessThreshold() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Returns the actual value of compactness threshold.
getComplexKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Generates the sinus filter mask of the complex part of the Gabor filter.
getCompression() - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane: Get compression option
getCompression() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Get the compression type
getCOMx() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns the center of mass of the snake in x-direction.
getCOMy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns the center of mass of the snake in y-direction.
getConcaveness(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
getConcavenessValues() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
getCondition() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
getCondition() - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.ConditionalDistribution: Get conditional variable
getCondition() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
getCondition() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
getConeAreas() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get areas of growth cone regions.
getConeLengths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get length of the growth cone region along the neurite skeleton graph without neurite shaft areas.
getConeRoundness() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get roundness of growth cone regions, 1 means a perfect circle.
getConeSpineCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get number of spines (filopodia-like protrusions) per growth cones.
getConfigValue(String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig: This function reads out the value of a given environment property.
getConfigWin(ALDOperator, ALDOpParameterUpdateEventListener) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorCollection
getConnectivity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Query the connectivity of pixels within border.
getConnectorIDs() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Get connector IDs.
getContinuousDOF() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState: Get continuous dimensions of target state in continuous
getContinuousDOF() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory: Get number of continuous state variables
getContour() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Get a Contour2D copy of this object.
getContour() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Method to get the contour object from the current 2D region.
getContour() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Get a reference to the contour.
getContour2DAsXml(MTBContour2D, MTBXMLContour2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Copy the information of contour into the corresponding xml element xmlContour.
getContour2DFromXml(MTBXMLContour2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Get a new MTBContour2D from the information of the xmlContour.
getContourID() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Get the contour ID.
getContourImg(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Create a new image where all contour pixels of img are set to 1, all other pixels to 0.
getContourLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Calculates the length of the outer contour using it's chaincode.
getContourPoints(int, int, int, int, int) - Static method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing: Computes both points perpendicular to the vector x1,x2 with distance 'distance'.
getContours() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Returns extracted contours.
getContourSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI: Get 2D contour set from Roi.
getContourSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Reads a ROI manager selection into a set of contours.
getContourType() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Get reference to the current contour type.
getCoordinatesNeighborNeighbors(int, int, int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
getCorrCircularity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Calculates corrected circularity of given region.
getCorrectGamma() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Get flag to use gamma correction.
getCorrelationImages() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Compute the correlation images as specified by the parameters.
getCorrelationThreshold() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Get threshold for thresholding wavelet correlation images
getCost() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Get edge cost as double value.
getCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
getCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution: Returns the covariance matrix
getCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
getCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
getCovariance() - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.SecondOrderCentralMoment
getCovariance() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
getCovariance() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
getCovariance() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
getCovariance() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
getCreateColorImageFlag() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Get the flag that determines the creation of an image with randomly colored regions.
getCreateLabelImageFlag() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Get the flag that determines the creation of an image with region labels.
getCurGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Returns current gamma vector.
getCurrentMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Extracts currently selected mode, i.e. data source.
getCurrentOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Get the current overlap mask.
getCurrentSlice() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get a copy of the current slice.
getCurrentSlice(MTBOperator) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get a copy of the current slice.
getCurrentSliceCoords() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the current slice coordinates (z,t,c) (for functions that work on a slice only, this has nothing to do with the ij.ImageStack's current slice)
getCurrentSliceIndex() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the current slice index (for functions that work on a slice only, this has nothing to do with the ij.ImageStack's current slice)
getCurrentSliceLabel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the slice label of the slice specified by the current slice index
getCurrentSliceLabel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Get the slice label of the slice specified by the actual slice index
getCurrentSliceLabel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Get the slice label of the slice specified by the actual slice index
getCurrentSliceLabel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get the slice label of the slice specified by the actual slice index
getCurrentSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Returns a copy of the current snake.
getCurrentSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Returns a copy of the current snake(s).
getCurrentSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Returns a copy of the set of current snakes.
getCurrentSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Returns a set with current snake(!).
getCurrentTime() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: Get the current time index, i.e. the time index that was assigned to the latest added information
getCurrentZStackCoords() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the current z-stack coordinates. [0]=t-coordinate, [1]=c-coordinate.
getCurvature(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Curvature at point (x,y,z).
getCurvature(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: compute the curvature at at nearest contourpoint to (x,y,z) if x or y are not in the boundaries it returns 0 if z is not in the boundaries it returns the 2d cuvature
getCurvatureInfoImage() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Access info image about curvature analysis.
getCytoplasmResult() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Returns reference to cytoplasm/cell boundary detection result.
getData() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel: Returns the data read from GUI or file.
getData(Class<?>) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
getData() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel: Returns the data read from GUI or file.
getData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Get data for current MTBGraphEdge.
getData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Get data of MTBGraphNode.
getData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
getData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: Returns a reference to the data associated with the node.
getDataLabels() - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans: Get assigned labels.
getDate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get current date for result dirs.
getDebug() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Get value of debug.
getDebug() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of debug.
getDebug() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Get value of debug.
getDefinedSpineLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get length to define a neurite branch as spine (filopodia-like protrusions).
getDelimiter() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Returns the currently chosen delimiter.
getDeltaApproximator() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives: Get reference to delta function approximator.
getDeltaT() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives: Get step size.
getDeltaX() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
getDeltaXY() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
getDeltaY() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
getDeltaZ() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
getDenoise() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Get the denoising flag. true if denoising is activated.
getDerivative(MTBSegmentationInterface, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Returns the energy derivative value at position (x,y,z).
getDerivative(MTBSegmentationInterface, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Returns the energy derivative value at position (x,y,z).
getDerivative(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
getDerivative(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
getDerivative(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
getDerivative(MTBLevelsetFunctionDerivable, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable: Get the energy derivative value, i.e. velocity, for position (x,y,z).
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Updates the fitting term based on new region average values.
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Updates matrix A given weights for the internal energy term.
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Updates matrix A given weights for the internal energy term.
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Updates the region coupling energy term in matrix A.
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable: Returns the linear matrix part of this energy for snake optimization.
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable: Returns the vector part of this energy for snake optimization.
getDerivativeWithoutDelta(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
getDerivativeWithoutDelta(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
getDerivativeWithoutDelta(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
getDerivativeWithoutDelta(MTBLevelsetFunctionDerivable, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable: Get the energy derivative value, i.e. velocity, for position (x,y,z).
getDerivativeX(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Partial derivative in x direction at position (x,y,z).
getDerivativeX(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance: Get x-derivative of the distance map at given position using central differences.
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient: Get x-derivative of negative absolute gradient value to the power of two (external energy) at given position using central differences.
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D: Get x-derivative of external snake energy at given position.
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity: Get x-derivative of external snake energy at given position using central differences.
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Get x-derivative of external snake energy at given position.
getDerivativeX_norm(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Get x-derivative of external snake energy at given position on a normalizes image coordinates in range [width*scale, height*scale].
getDerivativeXX(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Second partial derivative in x direction at position (x,y,z).
getDerivativeXX(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: computes the the derivation in x direction 2 times at nearest contourpoint to (x,y,z)
getDerivativeXY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Second partial derivative in x-y direction at position (x,y,z).
getDerivativeXY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: computes the the derivation in x and y direction at nearest contourpoint to (x,y,z)
getDerivativeXZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Second partial derivative in x-z direction at position (x,y,z).
getDerivativeXZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: computes the the derivation in x and z direction at nearest contourpoint to (x,y,z)
getDerivativeY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Partial derivative in y direction at position (x,y,z).
getDerivativeY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance: Get y-derivative of the distance map at given position using central differences.
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient: Get y-derivative of negative absolute gradient value to the power of two (external energy) at given position using central differences.
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D: Get y-derivative of external snake energy at given position.
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity: Get y-derivative of external snake energy at given position using central differences.
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Get y-derivative of external snake energy at given position.
getDerivativeY_norm(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Get y-derivative of external snake energy at given position on a normalizes image coordinates in range [width*scale, height*scale].
getDerivativeYY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Second partial derivative in y direction at position (x,y,z).
getDerivativeYY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: computes the the derivation in y direction 2 times at nearest contourpoint to (x,y,z)
getDerivativeYZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Second partial derivative in y-z direction at position (x,y,z).
getDerivativeYZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: computes the the derivation in y and z direction at nearest contourpoint to (x,y,z)
getDerivativeZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Partial derivative in z direction at position (x,y,z).
getDerivativeZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
getDerivativeZZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Second partial derivative in z direction at position (x,y,z).
getDerivativeZZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: computes the the derivation in z direction 2 times at nearest contourpoint to (x,y,z)
getDescription() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components.MTBTableWindow.DataTabFileFilter
getDescription() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapterRIU
getDescription() - Method in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
getDestinationImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Get value of Input argument DestinationImage.
getDetailedInProResults() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Access detailed information on indentations and protrusions.
getDetectedNeurites() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get vector of detected neurite sets for each image.
getDetectedNeuritesSet() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get set of detected neurites.
getDetectedParticles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D: Get regions of detected particles.
getDetectionResults() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Get the detection results.
getDetectionResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Get the result table of the detected neurites.
getDetectorMode() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get current detector mode.
getDetectors() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Get a reference to configured detectors' vector.
getDiagonalNeighbors() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Get value of Parameter argument DiagonalNeighbors.
getDiagonalNeighborsFlag() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Get the neighborhood flag.
getDiameter() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
getDiffX_image() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Calculate the image from the first order partial derivative in x-direction from the vectors U.
getDiffY_image() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Calculate the image from the first order partial derivative in y-direction from the vectors V.
getDimension() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Returns the dimension of the given membership.
getDimension() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: Returns the dimension of the given membership.
getDimension() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Returns the dimension of the segmentation.
getDimension() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
getDimension() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns the dimension of the given membership.
getDimensionality() - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult: Returns the dimension of the result object.
getDimensionality() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
getDimensionality() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
getDimensionality() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
getDimensionOfScope() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.DistanceTargetFunction
getDimensionOfScope() - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
getDirDialog - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel: File/directory chooser dialogue.
getDirection(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Get direction of the vector at position (x,y) in the vector field.
getDirectionalDifferences(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
getDirectionalities(Hashtable<Integer, Vector<Double>>, Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
getDirections() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
getDirectoryName() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputData: Returns current name of directory.
getDirName() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel: Get directory for processing.
getDistance(MTBRegion2D, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
getDistanceAlgebraic(Collection<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Returns the algebraic distance of the given point set.
getDistanceEuclideanPointToEllipse(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Returns the Euclidean distance of a point to an ellipse.
getDistanceImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
getDistanceImage() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Get the calculated distance map image.
getDistanceMap() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Get the calculated distance map.
getDistances() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
getDistImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Returns calculated distance map.
getDistMatrix(MTBRegion2DSet, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
getDistMetric() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Get the used distance metric.
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorEigenStructures
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPs
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPsRIU
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
getDoErosion() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Get value of doErosion.
getDomainXMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns maximal x coordinate represented in class map.
getDomainXMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns minimal x coordinate represented in class map.
getDomainYMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns maximal y coordinate represented in visibility map.
getDomainYMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns minimal y coordinate represented in class map.
getDrawType() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Get the kind of region image drawn by the operator
getEccentricity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Calculates eccentricity of the region in the range of [0,1].
getEdgeNum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Get number of included MTBGraphEdges.
getEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Get all edges of the MTBGraph.
getEigenvalueDecompositionAt(int, int) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Get eigenvalue decomposition of of the Hessian matrix to get largest eigenvalue at pixel (x,y) to get the vector perpendicular to the vessel path and eigenvalues.
getEigenvalues() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Get calculated eigenvalues in ascending order.
getEigenvects() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Get calculated eigenvectors, one vector per column, in ascending order.
getElapsedTime() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime: Returns the elapsed time since last reset (or invoking the constructor) in seconds
getElement(NodeList, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
getElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Returns the element at the specified position in this list.
getElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet: Returns the element at the specified position in this list.
getEllipsoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Returns set of initial snake ellipses.
getEndCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get number of end points.
getEndNodes() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get all end nodes of the MTBNeuriteSkelGraph.
getEndPoint() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine: Get the end point of the line segment.
getEnergies() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Returns a reference to the list of energies.
getEnergy() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get external snake energy label.
getEnergy(int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy: Returns the energy with given index.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: Returns element i of the energy list.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Returns element i of the energy list.
getEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of energy.
getEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Get value of energy.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable: Returns element i of the energy list.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable: Returns element i of the energy list.
getEnergyDerivativeMaxVal() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Returns the maximum possible derivative value this energy may yield.
getEnergyDerivativeMaxVal() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Returns the maximum possible derivative value this energy may yield.
getEnergyDerivativeMinVal() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Returns the minimum possible derivative value this energy may yield.
getEnergyDerivativeMinVal() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Returns the minimum possible derivative value this energy may yield.
getEnergyLabel() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get energy label for external energy, used for optimization.
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: Returns the list of energies.
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Returns the list of level set energies.
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable: Returns list of energies with actual type.
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
getEnergySet() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives: Get set of energies.
getEnergySet() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Returns a reference to the set of energies.
getEnergySet() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
getEnergySet() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
getEnergyValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Get current energy value for the snake.
getEntireTargetIDs() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: Get the targetIDs of all targets that ever existed up to current time.
getEntropyImage() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
getEntropyMeanDifference(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
getEnvVarValue(String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig: This function reads out the value of a given environment variable.
getEpsilon() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives: Get epsilon for Heaviside function approximation.
getEquatorLength() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Get equator length.
getErodeSize() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Get value of erodeSize.
getErodeSize() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: The size of the eroding element.
getError() - Method in exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DException
getError() - Method in exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2DException
getError() - Method in exception de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2DException
getError() - Method in exception de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphException
getError() - Method in exception de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DException: Returns the complete exception message as string.
getESSPercentage() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA: If this percentage of number of samples is below the current effective sample size (ESS), the samples are resampled.
getEstimatedCurve() - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet: Get estimated curve.
getEstimatedCurve() - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet: Get estimated curve.
getExceptionID() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException
getExceptionID() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBException
getExceptionID() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBImageException
getExcluded() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
getExcluded() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
getExcludeMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Returns the current exclude mask.
getExcludeMask() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
getExistingTargetIDs() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
getExistingTargetIDs(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: Get the targetIDs of all targets existing at time t.
getExtEnergyInit() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Calculate the initial image for the external energy of the snake.
getExtension(String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator: Get extension from filename if any.
getExtractedNeurites() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Get extracted neurites as result of the NeuriteExtraction2D operator.
getFactory() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState: Get associated factory
getFactoryMethod() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getFeatureLines() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get neurite corresponding feature lines of borders between soma and neurite shafts and neurite shafts and growth cones.
getFeatureOp() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBP: Get instance of actual feature calculator.
getFeatureOp() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Get instance of actual feature calculator.
getFeatureOp() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIU
getFeatureOps() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures
getFeatureOps() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPs
getFeatureOps() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPsRIU
getFeatureOps() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorTiles: Method to request operators for feature extraction to be applied.
getFeaturePoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get neurite corresponding feature points of borders between soma and neurite shafts and neurite shafts and growth cones.
getFGValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Get foreground value
getFieldSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
getFieldSizeX() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Get the field size in x-direction.
getFieldSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
getFieldSizeY() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Get the field size in y-direction.
getFileList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree: Collect all files in the directory tree including their complete paths.
getFileList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData: Get the list of all files inside the directory.
getFileName() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Get the filename of the image that has to be read.
getFileName() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Get image filename
getFileName(String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator: Returns the file name without leading directories or file description (extension).
getFilterImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Get flag to use gaussian filter.
getFilterMode() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Get filter mode to define relation of foreground to background.
getFilterResponseStack() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Get individual filter responses.
getFirst() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Returns the first element in this list.
getfirstFeatureAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get first feature of neurite corresponding feature points from borders between soma and neurite shafts.
getForeground() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Get the used foreground color.
getForegroundSum() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
getFps() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Get the frames per second for movie writers (*.avi,*.mov).
getFramesPerSecond() - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane: Get fps option
getGamma() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Get gamma correction value.
getGamma() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Get the gamma value.
getGammaToAuto() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Get if gamma should be calculated automatically or not.
getGaussianKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Generates the Gaussian part of the Gabor kernel for a given orientation.
getGaussKernel() - Method in class de.unihalle.informatik.MiToBo.math.arrays.filter.GaussFilterDouble1D: Get normalized Gaussian kernel for given parameters.
getGaussKernelC() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get Gaussian kernel image (non-normalized) in c-dimension for given parameters, null if sigma is zero in c-dimension
getGaussKernelT() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get Gaussian kernel image (non-normalized) in t-dimension for given parameters, null if sigma is zero in t-dimension
getGaussKernelX() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get Gaussian kernel image (non-normalized) in x-dimension for given parameters, null if sigma is zero in x-dimension
getGaussKernelY() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get Gaussian kernel image (non-normalized) in y-dimension for given parameters, null if sigma is zero in y-dimension
getGaussKernelZ() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get Gaussian kernel image (non-normalized) in z-dimension for given parameters, null if sigma is zero in z-dimension
getGaussMixture(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
getGenericEnergyList() - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy: Returns list of energies converted to generic type.
getGenericEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Returns the list of energies.
getGenericEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable: Returns the list of energies.
getGenericEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable: Returns the list of energies.
getGradientMode() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Get the used gradient mode for field calculation.
getGraphCost() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Get total amount of the graph costs.
getGraphNode(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning: Get the graph node from partition 'partitionID' in subgraph 'subgraphID'.
getGrayValue() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
getGrayValue() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Get the gray value of the regions in a mask image (MASK_IMAGE only).
getGrownRegions() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Returns a MTBImageByte image after growing.
getGrowthConeRegions() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get regions of the separated growth cones.
getGtContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: Get list of groundtruth contours.
getGVF() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D: Get the calculated Gradient Vector Flow field.
getH() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D: Get current h-parameter (max height of the h-domes).
getHeatmapImage() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Returns the result color heat map.
getHeight() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get skeleton graph image size in y direction.
getHeight() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Get image height.
getHeight() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Get image height.
getHeight() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Get image height.
getHeight() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Get image height.
getHeight() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Get height of level set function.
getHistogram() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
getHistoryLink(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess: Gets the port to which the object is currently linked in history.
getHueMTBImg() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Get the hue channel image.
getHueThresh() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Return the treshold for the hue channel.
getIcon() - Method in class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon: Get reference to the icon.
getID() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
getID() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Return the ID of the region.
getID() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Return the ID of the region.
getID() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D: Return the ID of the region.
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBImageException
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBLevelsetException
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBSnakeException
getIDImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Get image of region ID (of type MTB_BYTE).
getIgnoreInvalidStackSpecification() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Get the flag to ignore an invalid stack specification.
getImageBox(Object) - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess: Gets the image container associated with the given image object.
getImageCount() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Get the number of (multi-dimensional) images stored in the specified file.
getImageDerivatives() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Calculate second partial derivatives of the input image to generate Hessian matrix at each pixel position and getting the vector perpendicular to the vessel path.
getImageFiles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get vector of all image files included in the experiment folder for detection.
getImageID(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Get the ID of the imageIdx-th image in the file, if available
getImageJPropValue(String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig: This function reads out the value of a given ImageJ preference.
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
getImageName() - Method in interface de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Interface: Returns the name of the processed image.
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Note: Returned string might be null if the result is associated with a single cell rather than a complete image!
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel: Note: Returned string might be null if the result is associated with a single cell rather than a complete image!
getImageName(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Get the name of the imageIdx-th image in the file, if available
getImageObject() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowButton: Returns the image object associated with the button.
getImagePart(int, int, int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get a copy of a part of this image as new MTBImage.
getImagePart(MTBOperator, int, int, int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get a copy of a part of this image as new MTBImage.
getImagePart(MTBImage, int, int, int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory: Get a copy of a part of this image as new MTBImage
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox: Gets the stored ImagePlus.
getImageShowButton() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowPanel: Returns the button object associated with the panel.
getImageSizeX() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D: Get the image size in x-direction.
getImageSizeY() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D: Get the image size in y-direction.
getImageType() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection: Get output image type.
getImageType() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Get the datatype of the resulting image.
getImg() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Get reference to the (input) image.
getInConst() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
getIndentationSegments() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Get list of indentation segments.
getIndex() - Method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel: The index of this channel.
getIndexMap() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Get map of indices of maximal responses.
getIndexOfImageToRead() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Get the index of the image that has to be read from the file.
getInEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Get input edges for node.
getInflectionPoints() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Get list of inflection points.
getInfo() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: Get info string.
getInfo() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
getInfoImage() - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Get the info image with analysis data visualized.
getInImg() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getInImg() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Get value of Input argument inImg.
getInImg() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Get the input image.
getInImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of inImg.
getInImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer: Get input image.
getInImg1() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
getInImg2() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
getInitAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Get the initial alpha value.
getInitBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Get the initial beta value.
getInitBinImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of initBinImg.
getInitialGUIValue(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
getInitialGUIValue(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
getInitialSegmentation() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
getInitialSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver: Get initial segmentation.
getInitialSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Returns initial snake.
getInitLabelImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of initLabelImg.
getInitSegImageByte() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: Return the resulting initial segmentation image.
getInner(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Get a specific inner border.
getInner(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Get a specific inner contour from the contour object.
getInnerContourLengthMin() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Get the minimum number of pixels in the inner contour (length of the contour).
getInnerCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Get the number of inner contours including in the contour object.
getInputDir() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get directory of input images.
getInputImage(int) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Getter for the input image of specified layer.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get multichannel fluorescence input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Get input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Get input image
getInputImage() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Get the input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection: Get uneven illuminated input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Get low contrast input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Get the underlying input image of the gradient field..
getInputImage() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Get input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
getInputImage() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Get input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D: Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose: Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate: Get value of inImg.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode: Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen: Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat: Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor: Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Returns input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Get input image
getInputImage() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
getInputImagePlus() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Get ImagePlus that has to be stored to disk
getInputImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get input image.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Get input image.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get input image.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver: Get input image.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter: Get input image
getInputMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get input mode.
getInputMTBImage() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Get MTBImage that has to be stored to disk
getInputMTBImgRGB() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Returns the input image, null if not set.
getInputRegions() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Get reference to the input regions.
getInputRegions() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Get the regions that have to be drawn
getInputRegs() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Get set of input regions.
getInputTreelines(int) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Getter for the input treelines of the specified layer.
getInstance() - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon: Get singleton instance.
getInstance() - Static method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Single access point for singleton functionality.
getInstance() - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools: Single access point for singleton functionality.
getIntensityMeans() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
getIntensityNormalizationMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Request mode for normalizing image intensities.
getIntensityReport() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
getIntensityStdDevs(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
getIntermediateLS() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
getIntermediateLS() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Get value of intermediateLS.
getIntersection(MTBLineSegment2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D: Calculates the point of intersection between the segments.
getInvalidImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Get value of invalidImage.
getInvalidImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of invalidImg.
getInvalidTilesNum() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult: Get number of invalid tiles.
getInverseCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
getIterationCount() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Returns the current iteration count.
getIterationsPerSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Returns the total number of iterations per snake.
getJComponent() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
getJComponent() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
getJComponent() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.
getJComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
getJComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
getJmax() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Get Jmax
getJmax() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Get Jmax (maximum scale 2^Jmax - 1)
getJmin() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Get Jmin
getJVMPropValue(String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig: This function reads out the value of a given JVM property.
getK() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D: Calculates kernel for given angle and pre-defined sigma and length.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Calculates kernel for given angle and pre-defined sigmas.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D: Calculates Gaussian derivative kernel for given parameters.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Calculates Gaussian derivative kernel for given parameters.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D: Calculates kernel for the given orientation.
getKernelImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Get convolution kernel (image).
getKernelMask() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Get mask of valid kernel elements.
getKernelNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Get value of Parameter argument kernelNormalization.
getKernelOrigin() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Get value of Parameter argument kernelOrigin.
getKernels() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Get smoothing kernels
getKernelTruncation() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get kernel truncation factor.
getKey(HashMap<Integer, String>, String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils: Obtain the key for a given value of a HashMap, if available.
getKLower() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
getKolmogorovSmirnovStatistic(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
getKUpper() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
getLabel(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: returns the value of labelImg at position (x,y).
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Returns label mask with segmentation result.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Returns label image of detected nuclei.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Returns gray-scale label image with nuclei regions.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Get the label image.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Returns a label image visualizing the segmentation.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get the label image.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage: Get reference to the current Label image.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Get image of region labels (of type MTB_INT).
getLabelImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Get value of labelImg.
getLabelImg() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
getLabelMostInRegion(MTBRegion2D, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
getLabelsInRegion(MTBRegion2D, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
getLambda() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
getLambdaArray() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
getLambdaArray() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
getLargestNonEmptyBin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
getLast() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Returns the last element in this list.
getLayer() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Get the layer where the node is located.
getLayerSubsetForInputImages() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Request the set of layers from which to provide images to the operator.
getLayerSubsetForInputTreelines() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Request the set of layers from which to provide treelines to the operator.
getLBPCodeArrayRI(int) - Static method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs: Get array with LBP rotation invariant codes.
getLBPCodeArrayRIU(int) - Static method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs: Get array with LBP rotation invariant uniform codes.
getLBPHistogram(int, int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapter: Calculate the histogram of LBP codes in the neighborhood of the specified pixel.
getLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Get the length of the polygon.
getLevel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D: Return the tree level (level identifier).
getLineSegmentSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Reads ROI manager selections into a set of line segments.
getLinkageMode() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
getLogFaculty(int) - Method in class de.unihalle.informatik.MiToBo.math.LogFaculty: log(n!)
getLogFacultyFraction(int, int) - Method in class de.unihalle.informatik.MiToBo.math.LogFaculty: log(n1!
getLongestCommonPrefixes(Vector<String>) - Static method in class de.unihalle.informatik.MiToBo.tools.strings.StringAnalysis: Extracts the set of all prefixes shared by at least two strings in the given set.
getLongestPath(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get the pixels of the longest path of the neurite skeleton graph.
getLowerBound() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools: Get lower bound of the normalization to range [lowerBound, upperBound].
getLPB16(int, int, double) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal: Extract codes for 16-pixel neighborhood with r=2.
getLPB24(int, int, double) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal: Extract codes for 24-pixel neighborhood with r=3.
getLPB8(int, int, double) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal: Extract codes for 8-pixel neighborhood with r=1.
getMagImage() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Calculate the gradient magnitude image from the vectors U and V.
getMagnitude(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Get magnitude of the vector at position (x,y) in the vector field.
getMajorAxisLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Calculates length of the major axis of the ellipse best fitting.
getMarker(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Returns a marker from the vector.
getMarkerFromPosition(Point, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Get marker closest to given point position in given slice.
getMask() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Returns binary mask with segmentation result.
getMask() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Returns binary mask with segmentation result.
getMask(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
getMask(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
getMask(int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Gets the mask of the specified class (0 Background, 255 Foreground)
getMask(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
getMask(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
getMaskFromNuclei(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
getMaskRadiusC() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Get value of Parameter argument maskRadiusC.
getMaskRadiusT() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Get value of Parameter argument maskRadiusT.
getMaskRadiusX() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Get value of Parameter argument maskRadiusX.
getMaskRadiusY() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Get value of Parameter argument maskRadiusY.
getMaskRadiusZ() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Get value of Parameter argument maskRadiusZ.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose: Returns the given mask size, 0 if not set.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate: Get value of masksize.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode: Returns the given mask size, 0 if not set.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen: Returns the given mask size, 0 if not set.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat: Get current masksize.
getMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite: Returns result matrix with matching result.
getMax() - Method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel: The maximum value of this channel.
getMaxAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt: Get the maximum value for parameter alpha.
getMaxAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
getMaxAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
getMaxBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt: Get the maximum value for parameter beta.
getMaxBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
getMaxBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
getMaxBinaryPattern() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapterRIU
getMaxDist() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
getMaxFragmentDistance() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get maximum neuron fragment distance in pixel.
getMaxFragmentDistance() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get maximum fragment distance , in pixel.
getMaximalComponentDist() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Returns the maximal component distance for linking.
getMaximalComponentSize() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Returns the maximal valid component size for component removal.
getMaxIter() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of maxIter.
getMaxIter() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff: Get maximum iteration count.
getMaxIter() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations: Get maximum iteration count.
getMaxIter() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff: Get maximum iteration count.
getMaxIterations() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get maximum number of iterations to stop detection.
getMaxIterations() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get maximum number of iterations to finish snake optimization,
getMaxIterations() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Get value of maxIterations.
getMaxIterations() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Get maximal number of iterations.
getMaxLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Returns the maximal label used in the membership representation.
getMaxLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: Returns the maximal label used in the membership representation.
getMaxLabel() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Returns the maximal label used in the segmentation representation.
getMaxLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
getMaxLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns the maximal label used in the membership representation.
getMaxLevels() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Returns maximum number of levels in iterative mode.
getMaxN() - Method in class de.unihalle.informatik.MiToBo.math.LogFaculty
getMaxSpineLength() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get maximum length of a spine (filopodia-like protrusion) in pixel.
getMaxSpineLength() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get maximum length of a spine, in pixel.
getMaxSpineLength() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Get maximum length of a spine (filopodia-like protrusion) in pixel.
getMaxValue() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
getMaxValueBin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
getMaxVoronoiExpandDist() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Returns the maximal distance of pixels considered in Voronoi expansion.
getMaxWeight() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
getMean() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution: Returns the mean vector.
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
getMean() - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.FirstOrderMoment
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
getMeanBackgroundIntensity() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
getMeanKernelC() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get mean kernel image (non-normalized) in c-dimension for given parameters, null if size is zero in c-dimension
getMeanKernelT() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get mean kernel image (non-normalized) in t-dimension for given parameters, null if size is zero in t-dimension
getMeanKernelX() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get mean kernel image (non-normalized) in x-dimension for given parameters, null if size is zero in x-dimension
getMeanKernelY() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get mean kernel image (non-normalized) in y-dimension for given parameters, null if size is zero in y-dimension
getMeanKernelZ() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get mean kernel image (non-normalized) in z-dimension for given parameters, null if size is zero in z-dimension
getMeans() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Returns the average region intensities last calculated.
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
getMeasurementUnit() - Method in interface de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Interface: Returns the unit of measurements.
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
getMemorizedMatrixA() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Returns matrix carrying always the values of the last iteration, or null before first run.
getMin() - Method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel: The minimum value of this channel.
getMinAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt: Get the minimum value for parameter alpha.
getMinAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
getMinAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
getMinAreaAfterErosion() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
getMinAreaAfterOpening() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
getminAreaSeedRegions() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
getMinBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt: Get the minimum value for parameter beta.
getMinBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
getMinBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
getMinCompactness() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
getMinimalComponentSize() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Returns the minimal valid component size for component removal.
getMinMaxCoordinates() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Extracts the extreme coordinates of the region in each dimension.
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get minimum and maximum value of the image (all channels) as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Get minimum and maximum value of the image as double
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Get minimum and maximum value of the image as int
getMinorAxisLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Calculates length of the minor axis of the ellipse best fitting.
getMinRegionArea() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
getMinRegionSize() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Get the minimum size of detected regions.
getMinSize() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Get value of minSize.
getMinSizeFraction() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Get value of minSizeFraction.
getMinWeight() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
getMode() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat: Get the desired operator mode.
getModification() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
getMoelculeImg() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D: Get the input image with the fluorescence labeled molecules.
getMoleculeChannles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D: Get molecule channels, used for extraction.
getMoleculeChannles() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Get molecule channels, used for molecular profile extraction.
getMolecules() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Get names of molecules for each image channel.
getMoment(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Calculate moment of the region of order p,q.
getMoment(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
getMorphOp() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection: Get morphological operation for illumination correction, default is closing.
getMotionFraction() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get minimum fraction of point motion to stop detection.
getMotionFraction() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get minimum motion fraction of snake control points, to finish snake optimization.
getMotionFraction() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff: Get motion fraction.
getMSERs() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Returns set of detected MSERs.
GetMTBContour2DSetFromXSVFiles - Class in de.unihalle.informatik.MiToBo.io.importer: Read a MTBContour2DSet from a list of ASCII xSV files.
GetMTBContour2DSetFromXSVFiles() - Constructor for class de.unihalle.informatik.MiToBo.io.importer.GetMTBContour2DSetFromXSVFiles: Default constructor.
getMTBImage() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox: Gets the stored MTBImage.
getMTBImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Creates a bi-level MTBImageShort of the level set function.
getMTBImageLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Creates a MTBImageShort of the level set function.
getMultiphase() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of multiphase.
getNarrowBandWidth() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Get width of narrow band.
getNarrowIterator() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: get an iterator through narrow band
getNeighbors() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Get all neighbors of the current node.
getNeighbourhood() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
getNetDirections() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
getNetDistances() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
getNeurite() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
getNeuriteColor() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get neurite region color (RGB) for result image.
getNeuriteColor() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get neurite region color (RGB) for result image.
getNeuriteDetector() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Get current neurite detector.
getNeuriteFeatures(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Method to calculate the neurite features from the neurite width profile.
getNeuriteGraph() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get neurite corresponding skeleton graph.
getNeuriteImage(Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet: Visualize the neurites skeleton graphs and regions.
getNeuriteMaskSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get neurite mask size in pixel.
getNeuriteMaskSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get maximum neurite mask size, in pixel.
getNeuriteMaskSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Get neurite mask size in pixel.
getNeuriteRegion() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get neurite corresponding region.
getNeuriteSet() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D: Get the input set of neurites.
getNeuriteSet() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D: Get the input set of neurites.
getNeuriteShaftArea() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get area of neurite shaft region (without growth cone).
getNeuriteShaftRegion() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get neurite shaft region (without growth cone).
getNeuriteStack(Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet: Visualize the neurites skeleton graphs and regions.
getNeuriteWidths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get average widths of each neurite branch, including the average widths of the whole branches, the shafts and the growth cones.
getNeuronChannles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get neuron channels, used for detection.
getNeuronChannles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get neuron channels, used for detection.
getNeuronColor() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Get binary neuron color.
getNeuronImage() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Get input image of the binary neuron.
getNewConfigWin(ALDOperator, ALDGrappaWorkbenchTab.ParameterUpdateListener) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab
getNewConfigWin(ALDOperator) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorGUIExecutionProxy
getNewIndent(String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Return a new indentation string.
getNiblackConstant() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get niblack constant.
getNiblackConstant() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get Niblack thresholding constant.
getNode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData: Return the node object containing the data.
getNodeListFromTag(Document, String) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
getNodeNum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Get number of included MTBGraphNodes.
getNodes() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Get all nodes of the MTBGraph.
getNodes() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
getNodes() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix: Get graph nodes
getNodeType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
getNoiseCovariance() - Method in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
getNorm() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D: Calculates the Euclidean norm of the segment.
getNormal(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Get normal vector between two points.
getNormalCentralMoment(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Calculate normalized central moment of the region of order p,q.
getNormalizationFactor(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
getNormalizationFactor(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
getNormalizationMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Returns energy normalization mode.
getNormalizedCumulativeHistogram(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Create a normalized cumulative histogram from an image
getNormalizedImageHisto() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics: Extracts the normalized image histogram with 256 bins.
getNormedMagImage() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Normalize the gradient magnitude values into a range of [0,1].
getNRSCandidates() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Returns possible peak locations from NucleusRegionSeperator.
getNRSDistImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Returns distance image calculated intermediately.
getNRSEllipsoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Creates and returns a set of polygons as starting regions for snake analysis based on hypothesized ellipses from nucleus information
getNRSResultAreas() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Returns set of result regions from region separator.
getNRSResultCenters() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Returns set of detected region centers from region separator.
getNRSVoronoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Creates and returns a set of polygons as starting regions for the snakes.
getNucDetector() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Get detector for nuclei.
getNucleiAvgSize() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Returns average size of detected nuclei.
getNucleiChannel() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get image channel of nuclei.
getNucleiChannel() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get channel number, including the labeled nuclei.
getNucleiChannel() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Get nuclei channel number.
getNucleiCount() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Returns number of detected nuclei.
getNucleiRegions() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Returns set of detected regions.
getNucleiRegions() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Get detected nuclei regions.
getNucleiResult() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Returns nuclei detection result.
getNucleusRatio() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get ratio of nucleus pixels which should be included in an intact neuron region
getNucleusRatio() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get ratio of nucleus pixels which should be included in an intact neuron region
getNucleusSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get minimum nucleus size of nuclei regions
getNucleusSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get minimum nucleus size of nuclei regions
getNumberChannels() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Returns the number of image channels available.
getNumberOfClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Returns the number of classes represented in the membership.
getNumberOfClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: Returns the number of classes represented in the membership.
getNumberOfClasses() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Returns the number of classes represented by the segmentation.
getNumberOfClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
getNumberOfClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns the number of classes represented in the membership.
getNumberOfFrames() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
getNumberOfInEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Get number of incoming edges for MTBGraphNode.
getNumberOfMSERs() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Returns number of detected MSERs.
getNumberOfOutEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Get number of outgoing edges for MTBGraphNode.
getNumberOfStates() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState: Get number of states
getNumberOfStates() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
getNumEntries() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
getNumericalValue(int) - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult: Returns a numerical value representing the requested result component.
getNumericalValue(int) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
getNumericalValue(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
getNumericalValue(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
getNumIterations() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
getNumIterations() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Get number of iterations for the GVF field.
getNumIterations() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of numIterations Explanation: Number of iterations performed
getNumIterations() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Get value of numIterations Explanation: Number of iterations performed
getNumOfComponents() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
getNumOfImages() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
getNumOfIndeps() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
getNumOfIndeps() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
getNumOfIndeps() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
getNumOfParticles() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Get number of particles
getNumPhases() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Return .e. number phases.
getNx() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
getNx() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
getNy() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
getNy() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
getObjectsMeans(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
getObjectsStdDevs(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
getObservationDistribution() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
getObservationDistribution() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetPredictionFilterIndep
getObservationMatrices() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
getObservations() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
getObservations(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: Get the observations of time t.
getOldId() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D: Get previous index of snake point from the previous snake.
getOnlySelectedTreelines() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Ask operator if only selected or all treelines should be provided.
getOpeningSESize() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
getOperation() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime: Return UserTime or RealTime depending on mode of operation
getOperationType() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Get the operation type which should be applied to the input vector field.
getOperatorWorkingMode() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Request working mode of the operator, i.e., how the operator deals with treelines.
getOpIdentifier() - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult: Method returns an identifier characterizing the operator.
getOpIdentifier() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
getOpIdentifier() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
getOpIdentifier() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
getOpMode() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Get value of opMode.
getOptimalNeighbor(MTBGraphNode<PartitGraphNodeID>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning: Get node of partition 'partitionID' which is connected to current node and has optimal weight
getOrientation(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D: Deprecated.
getOrientation() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Get orientation.
getOrientation() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Calculates the orientation of the principal axis of the MTBRegion2D.
getOtsuRegs() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Returns set of regions resulting from Otsu thresholding.
getOtsuThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu: Get the resulting threshold.
getOutEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Get outgoing edges for node.
getOuterContours(MTBRegion2DSet, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Calculate the outer contours of the given regions in a image.
getOutImageType() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Get the type of image object that is created as result image.
getOutline() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape: Get outline of shape.
getOutputDir() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get directory of output results.
getOutputImage() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Get medialness filter image.
getOutputObservations() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM: Get a copy of the input observations with IDs set corresponding to the tracking results after GreedyGourmetPartitioning of the track graph constructed from the RBMCDA samples.
getOutputSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner: Get cloned snake object.
getOutputType() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter: Get output image type
getOverlaps() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
getOverwrite() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Get the overwrite permission flag
getParameterA() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Get value of implicit parameter a.
getParameterB() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Get value of implicit parameter b.
getParameterC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Get value of implicit parameter c.
getParameterD() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Get value of implicit parameter d.
getParameterE() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Get value of implicit parameter e.
getParameterF() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Get value of implicit parameter f.
getParent() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: Get the parent of this node.
getParentID() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
getPartChannel() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Get particle channel number.
getPartDetector() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Get detector for particles.
getPartialDiffX() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Calculate first order partial derivative in x-direction using central differences.
getPartialDiffX(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Get approximation of partial derivative in x-direction at point with given index.
getPartialDiffX_forward() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Calculate first order partial derivative in x-direction using forward differences.
getPartialDiffX_sobel() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Calculate first order partial derivative in x-direction using Sobel.
getPartialDiffY() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Calculate first order partial derivative in y-direction using central differences.
getPartialDiffY(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Get approximation of partial derivative in y-direction at point with given index.
getPartialDiffY_forward() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Calculate first order partial derivative in y-direction using forward differences.
getPartialDiffY_sobel() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Calculate first order partial derivative in y-direction using Sobel.
getParticle(int) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Get idx-th particle
getParticleAvgSize() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Returns average size of detected particles.
getParticleChannel() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D: Get image channel including particles.
getParticleCount() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Returns number of detected particles.
getParticleDetector() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D: Get particle detector.
getParticleDetector2D() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
getParticleRegions() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Get detected particle regions.
getParticleResult(int) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Returns number of detected particles per channel.
getParticles() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Get particles
getPath(Vector<Point2D.Double>, MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Internal method to traverse the path and return the pixel list.
getPath() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData: Request path associated with the node.
getPdf(int) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
getPerCellAvgSize() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Returns detected particle average size per cell.
getPerCellCount() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Returns detected particles per cell.
getPersistences(Hashtable<Integer, Vector<Double>>, Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
getPhase(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Return phase for a pixel/voxel
getPhase(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Return phase for a pixel/voxel, z coordinate defaults to zero
getPhaseCheckXY(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Return phase for a pixel checking limits of all coordinates.
getPhaseCheckXYZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Return phase for a pixel/voxel checking limits of all coordinates.
getPhi() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives: Get current level set function.
getPhi() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Get value of phi.
getPhiColorImage2D(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Get visualization of current level set function in red-blue color map.
getPhiImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Get visualization of current level set function.
getPixelInside() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Return number of pixels of all object phases.
getPixelOutside() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Return number of pixels of background phase.
getPixelsAlongSegment() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D: Calculates the set of integer pixel positions along the a segment.
getPlastidRegions() - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT: Access detected plastid regions.
getPointAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Get a specific 2D point belonging to the border object.
getPointDist(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D: Deprecated.
getPointNum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Get the number of points of the border object.
getPointNum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Get the number of points from the polygon.
getPoints() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Get all points belonging to the border object.
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Get polygon points.
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Return all points of the region.
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Return the points which are included in the 3D region.
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D: Return the points which are included in the 3D region.
getPoisson2Gauss() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Get flag if input image with poisson noise is to be transformed to image with gaussian noise following J.
getPolygon() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Get a Polygon2D copy of this object.
getPolygon() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapePolygon: Get polygon representing the shape.
getPolygon2DFromXml(MTBXMLPolygon2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: * Get a new Polygon2D from the information of the xmlPolygon .
getPolygonSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI: Get 2D polygon set from Roi.
getPolygonSetFromRoiFile(String, boolean) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Reads an ImageJ roi file into a set of polygons/snakes.
getPolygonSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Reads ROI manager selections into a set of polygons/snakes.
getPolySet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Get the polygon set.
getPortHashAccessObject() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools: Returns access object for port hash.
getPotential() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Returns a copy of the potential field (for faster access!).
getPotential() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D: Get the energy potential field from this external energy.
getPotentialNewPhases2D(boolean, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
getPrecision() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc: Returns calculated precision.
getPrecisionClutter() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
getPrecisionTrackEnd() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
getPrecisionTrackSegment() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
getPrecisionTrackStart() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
getPrecursorMap() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Get the calculated precursor map.
getPrecursorSegment() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Get preceeding segment along contour.
getPredecessor() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
getPredecessorOnContour(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: gets the value of the nearest contourpoint to point (x,y,z)
getPreferredSize() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
getPreserveTopology() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of preserveTopology.
getPreserveTopology() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Get value of preserveTopology.
getPreviousEnergyValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Get old energy value for the snake at last iteration.
getPreviousSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Returns the previous snake.
getProcessedChannel() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Get the processed channel.
getProcessMode() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Get current process mode.
getProfile() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile: Get profile data of the neurite region.
getProfilePoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
getProfiles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D: Get the resulting set of neurite profiles.
getProfileSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
getProtrusionSegments() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Get list of protrusion segments.
getQuality() - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane: Get quality option
getQuality() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Get the quality (quicktime only)
getRadius() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Get the radius of the node.
getRadiusImage() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Returns supplemental radius image, null if not generated.
getRandom() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
getRandom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Get the random number generator which is responsable to draw each region in a random color (COLOR_IMAGE only).
getRankOpMode() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Get value of Parameter argument rankOpMode.
getRealKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Generates the cosine filter mask of the complex part of the Gabor filter.
getRecall() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc: Returns calculated recall.
getRecallClutter() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
getRecallTrackEnd() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
getRecallTrackSegment() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
getRecallTrackStart() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
getRegCenters() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Returns the centers of the nuclei sorted to their original regions.
getRegion(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Method to get the included region in a 2D contour as Region2D object.
getRegion() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Get a Region2D copy of this object.
getRegion() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D: Return the 2D region.
getRegion() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeRegion: Get region representing the shape.
getRegionCount() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Get number of regions in set.
getRegionID() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get the region id.
getRegionMeans() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Get average intensity array indexed with class labels for first channel.
getRegionMeansAllChannels() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Get average intensity array indexed with class labels for all channels.
getRegions() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Get set of segmented regions.
getRegions(MTBImage, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelAreasToRegions
getRegions(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelAreasToRegions
getRegions3D(MTBImage, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelAreasToRegions
getRegionSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI: Get 2D region set from Roi.
getRegionSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Get the region set.
getRegionSet() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get the region set.
getRegionSet() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
getRegionSetFromRoiFile(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Reads an ImageJ roi file into a set of regions.
getRegionSetFromRoiFile(String, double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Reads an ImageJ roi file into a set of regions.
getRegionSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Reads a ROI manager selection into a set of regions.
getRegionSizes() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Get array of region areas indexed with class labels for first channel.
getRegionsTree(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Build a tree of regions from binarized images.
getRegionVars() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Get intensity variance array indexed with class labels for first channel.
getRegionVarsAllChannels() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Get intensity variance array indexed with class labels for all channels.
getREngine() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get JRI R engine to run R as a single thread.
getREngine() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Get R engine.
getReport() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
getRepositoryTag(String) - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile: Returns the tag/release of the current jar.
getRepositoryTag() - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile: Returns the tag/release of the current checkout, as specified in a given info file.
getResampleConstant() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get snake point resampling constant.
getResampleConstant() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get constant for snake point resampling.
getResponseStack() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Returns stack with intermediate (non-binary) results.
getResult() - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult: Returns the result data object of the calculator.
getResult() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
getResult() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
getResult() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
getResult() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Get result data.
getResult() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Returns evaluation result data.
getResultAreas() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Returns separated regions sorted according to original regions.
getResultArray() - Method in class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D: Returns result array.
getResultBinaryCorrelationStack() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Get resulting binarized correlation image stack.
getResultBorders() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Get result borders.
getResultCellImg() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Returns (optional) result image with cell contours.
getResultCenters() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Returns centers of result regions.
getResultContourImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of ResultContourImage.
getResultContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Get reference to the calculated contours.
getResultCorrelationStack() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Get resulting correlation image stack.
getResultCosts() - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Returns the costs of the shortest path.
getResultData() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Returns result data object.
getResultData() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Returns result data object.
getResultData() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Get the result data, i.e. mask and related quantitative data.
getResultData() - Method in class de.unihalle.informatik.MiToBo.features.FeatureCalculator: Returns result data object.
getResultData() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Get the transformed dataset.
getResultData() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.MTBGroundtruthEvaluationData: Returns result data.
getResultDataAreaFractions() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Returns result data object with area fractions per cell.
getResultDataArray() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Returns extracted result data.
getResultDataAvgSize() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Returns result data object with average size per cell.
getResultDataCellSizes() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Returns result data object with areas per cell.
getResultDataCounts() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Returns result data object with counts per cell.
getResultDataObjectInvalid(int) - Method in class de.unihalle.informatik.MiToBo.features.FeatureCalculator: Helper method to allow for requesting invalid dummy results.
getResultDataObjectInvalid(int) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats
getResultDataObjectInvalid(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
getResultDataObjectInvalid(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
getResultDataObjectInvalid(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
getResultDataTotalSize() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Returns result data object with total structure size per cell.
getResultDir() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get directory of intermediate and final results.
getResultIdentifier(int) - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult: Method returns an identifier characterizing the related component of the result.
getResultIdentifier(int) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
getResultIdentifier(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
getResultIdentifier(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor: Returns postprocessed skeleton image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Get the result label image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D: Returns result image, i.e. the segmentation mask.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Returns RGB color image overlayed with nuclei contours.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Returns result image, i.e. the segmentation mask.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Get the gamma corrected image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching: Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization: Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection: Get illumination corrected result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Returns result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Get contrast enhanced result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
getResultImage() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Get image with result data.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Get result image of the operation on the vector field.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression: Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D: Get result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Get result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
getResultImage() - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Returns the result image with path overlay.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Get the result image after applying operator.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D: Get the resulting h-dome image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose: Returns the opened image, null if not available.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate: Get value of resultImg.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode: Returns the eroded image, null if not available.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen: Returns the opened image, null if not available.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat: Get the result image after applying the operator.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor: Returns the skeleton image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor: Returns post-processed skeleton image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.WatershedBinary: Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Get result image with extracted borders.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Get reference to the binary image with the calculated contours.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of ResultImage.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Get value of resultImage.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Get image with segmentation result overlay.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: Get the resulting image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker: Returns the generated image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter: Returns image with plotted snakes.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding: Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Get the result image
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Get the resulting thresholded image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: Returns the result color image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet: Get the resulting region image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Get result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D: Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet: Get the resulting region image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Get the resulting region image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage: Get result image.
getResultImagePlus() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Get resulting image that was read from disk.
getResultImageStack() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Returns stack with result segmentation images.
getResultImageType() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
getResultImageType() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
getResultImageType() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
getResultImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos: Get value of resultImg.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getResultImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get resulting image.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Get resulting image.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get resulting image.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Get value of Output argument resultImg.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
getResultImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer: Get result image.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter: Get result image
getResultImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Get result image.
getResultingConvexHulls() - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Get set of extracted convex hulls.
getResultingHullImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Get image with convex hulls plotted.
getResultingRegions() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Get the resulting regions.
getResultingRegionsets() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
getResultJunctions() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Get detected junctions.
getResultLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter: Returns result label image.
getResultLines() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Get detected lines.
getResultMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Get binary mask of segmentation result.
getResultMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker: Returns generated mask.
getResultMTBImage() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Returns the converted image, null if not available.
getResultMTBImage() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Get resulting image that was read from disk.
getResultPath() - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Returns the extracted shortest path as point list.
getResultRGB() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter: Returns the result RGB color.
getResults() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Get resulting regions (each detetection corresponds to a region)
getResultSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter: Returns resulting snake object.
getResultSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter: Returns resulting snake object.
getResultSnakeImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Returns image with snakes contours.
getResultSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter: Returns resulting snake objects.
getResultSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Returns the set of result snakes.
getResultsTable() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
getResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get the result table of the detected neurites.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get final result table of morphology measurements.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Get particle statistics.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Get table of calculated features.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult: Get result table.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Get evaluation results.
getResultTreelines(int) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Getter for the result treelines of a specific layer.
getResultValue() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics: Get result value;
getResultVec() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
getResultVectorOfCurvatures() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Get calculated curvatures.
getResultVesselMap() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Get result.
getResultXylemRegions() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Return the binary image after the post processing of the grown region image.
getRevisionFile() - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile: Request name of the revision file.
getRGBImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D: Flag to request a RGB image in any case.
getRGBResult() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter: Get RGB values.
getRGBResult() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter: Get RGB values.
getRGBValue() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
getRoot() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree: Access the root node.
getRoundnessThreshold() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Returns the currently active roundness threshold.
getRowCount() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
getRuntime() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
getSample(double[]) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Returns a sample in the range [0, 1] from a cumulative distribution given by the array cdf
getSample(double[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Returns a sample in the range [0, 1] from a cumulative distribution given by the array cdf
getSampleConditionalProb(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM: Get the probability of the associations of i-th sample at the time t conditional on previous associations and all observations up to time t.
getSampleInfo(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM: Get the sample info object of the i-th sample.
getSampleInfo() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample: Get the info object of this RBMCDA-sample
getSampleJointProb(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM: Get the joint probability of all associations of the i-th sample conditional on all observations, normalized by all samples' probabilities.
getSampleJointProbs() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM: Get the joint probability of all associations of all samples conditional on all observations, normalized by all samples' probabilities.
getSampleObservations(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM: Get a copy of the observations with IDs set corresponding to the i-th sample's tracking results.
getSatMTBImg() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Get the saturation channel image.
getSatTresh() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
getSaveIntermediateResultPath() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Returns path where to save intermediate results.
getScaleDown() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Get the scaling factor of the snake.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Get scaling factor.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Get scaling factor.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Get scaling factor.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Get scaling factor.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Get scaling factor.
getScaleFactor() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable: Get scaling factor.
getScaleFactor() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable: Get scaling factor.
getScaleIntervalSize() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Get the size of the scale interval for correlation images
getScaleMax() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Get maximum of scales.
getScaleMin() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Get minimum of scales.
getScaleNum() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Get number of scales.
getScratchArea() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
getScratchFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
getsecondFeatureAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get second feature of neurite corresponding feature points from borders between neurite shafts and growth cones.
getSeedPoints(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter: coarse segementation of input frame to localize cells
getSeedPoints(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter: coarse segmentation of input frame to localize cells
getSeedRegions() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
getSeErosionSize() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
getSegContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: Get list of segmentation contours.
getSegDim() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get target dimension.
getSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get the generated segmentation object.
getSegmentationMode() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Returns mode activated during segmentation.
getSegmentLength() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Returns desired segment length for resampling.
getSelection() - Method in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel: Get the currently selected radio button string
getSelections() - Method in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
getSelections() - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane: Returns a hash map with the absolute filename as key and the indices of images selected from the corresponding file.
getSemiLengthAxisA() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Get half-length of axis A.
getSemiLengthAxisB() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Get half-length of axis B.
getSeOpeningSize() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
getSettings() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
getShaftLengths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get neurite shaft lengths of all branches without growth cone areas.
getShape() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Get shape of marker.
getShape() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get the selected shape.
getShapeDimX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get extent of shape in x dimension.
getShapeDimY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get extent of shape in y dimension.
getShapeDimZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get extent of shape in z dimension.
getShapeFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer: calculate several shape features in one method
getShapeFeatures() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
getShapeForErosion() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
getShapeForOpening() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
getShapeMaskSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get size of shape mask in x dimension.
getShapeMaskSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get size of shape mask in y dimension.
getShapeMaskSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get size of shape mask in z dimension.
getShapePosX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get position of shape in x dimension.
getShapePosY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get position of shape in y dimension.
getShapePosZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get position of shape in z dimension.
getShapeReport() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
getShortestPath(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get the pixels of the shortest path of the neurite skeleton graph.
getShortName() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Get common short name of operator for GUI.
getShortName() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
getShortName() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
getSigmaC() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get standard deviation (sigma) in c-dimension.
getSigmaInterpretation() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get the mode of how sigmas are interpreted.
getSigmaT() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get standard deviation (sigma) in t-dimension.
getSigmaX() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get standard deviation (sigma) in x-dimension.
getSigmaY() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get standard deviation (sigma) in y-dimension.
getSigmaZ() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Get standard deviation (sigma) in z-dimension.
getSignedArea() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Calculates the signed area of simple (!)
getSimpleShapeFeatures() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: calculate several shape features in one method
getSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
getSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
getSize() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList: count number of elements
getSizeC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get size of c(hannel)-dimension
getSizeC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getSizeC() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get size of c(hannel)-dimension
getSizeC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get window size in c-dimension
getSizeC() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get standard deviation (size) in c-dimension.
getSizeDilation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Get value of sizeDilation.
getSizeNeighborhood() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
getSizeOpening() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Get value of sizeOpening.
getSizePhase(short) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Return the size, i.e. number of pixel/voxels of a phase.
getSizeStack() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get size of the underlying (ImageJ) stack which corresponds to the number of slices
getSizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get size of t(ime)-dimension
getSizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getSizeT() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get size of t(ime)-dimension
getSizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get window size in t-dimension
getSizeT() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get standard deviation (size) in t-dimension.
getSizeTH() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Get value of sizeTH.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get size of x-dimension
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getSizeX() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get size of x-dimension
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get window size in x-dimension
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Calculate the expansion in x-direction of the region.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
getSizeX() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get standard deviation (size) in x-dimension.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
getSizeX() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Returns the size of the segmentation domain in x direction.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Return X size of the level set function.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Get width of level set function.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get size of y-dimension
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getSizeY() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get size of y-dimension
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get window size in y-dimension
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Calculate the expansion in y-direction of the region.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
getSizeY() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get standard deviation (size) in y-dimension.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
getSizeY() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Returns the size of the segmentation domain in y direction.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Return Y size of the level set function.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Get height of level set function.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get size of z-dimension
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getSizeZ() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get size of z-dimension
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get window size in z-dimension
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Calculate the expansion in z-direction of the region.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Get standard deviation (size) in z-dimension.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
getSizeZ() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Returns the size of the segmentation domain in z direction.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Return Z size of the level set function.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Get depth of level set function.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
getSkeletonGraphNodes() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get all nodes of the MTBNeuriteSkelGraph as MTBNeuriteSkelGraphNodes.
getSkeletonInfoImage() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Access info image about skeleton analysis.
getSlice(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get a copy of the specified slice.
getSlice(MTBOperator, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get a copy of the specified slice.
getSlice(MTBImage, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory: Get a copy of the specified slice
getSliceLabel(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the slice label of the slice specified by (z,t,c)
getSmallestNonEmptyBin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
getSnakeControlPoints(MTBContour2D) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Method to get each 7th point of the initial contour as snake control point.
getSnakeIterCount() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get number snake iteration counts, used for optimization.
getSnakeNumber() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Returns the number of snakes currently managed.
getSnakePoints() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Get snake points as vector of SnakePoint2D objects.
getSnakeRegion(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get the region which is included in the snake contour.
getSnakes() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Returns the result snakes.
getSndPartialDiffX(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Get approximation of 2nd order partial derivative in x-direction.
getSndPartialDiffY(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Get approximation of 2nd order partial derivative in y-direction.
getSpacing() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of spacing.
getSpacingIntermediate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Get value of spacingIntermediate.
getSpeeds(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
getSpineCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Get number of spines (filopodia-like protrusions).
getSpinePaths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get the pixels of all spine paths of the neurite skeleton graph.
getSrcNode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Get source node of the MTBGraphEdge.
getStackWithIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Returns a stack with intermediate segmentation results.
getStartFrame() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
getStartNode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get the start node of the MTBNeuriteSkelGraph.
getStartPoint() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine: Get the start point of the line segment.
getStartPoints() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Get the skeleton start points of every single neurite from the inside of the coarse cell body region.
getStateContinuous(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState: Get the continuous part of the idx-th state (indices start from 0)
getStateContinuous(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
getStateDiscrete(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState: Get the discrete part of the idx-th state (indices start from 0)
getStateDiscrete(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
getStatus() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Get the status of the node (segment).
getStdDev() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
getStdDev(MTBImage) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Get standard deviation of the image
getStdDevBackgroundIntensity(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
getStepSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Get step size of snake movement.
getStepSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Get step size of snake point movement.
getStepsizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the stepsize in t-dimension (timestep)
getStepsizeT() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get the stepsize in t-dimension (timestep)
getStepsizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get the stepsize in t-dimension (timestep)
getStepsizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the physical size of a voxel (stepsize) in x-dimension
getStepsizeX() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get the physical size of a voxel (stepsize) in x-dimension
getStepsizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get the physical size of a voxel (stepsize) in x-dimension
getStepsizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the physical size of a voxel (stepsize) in y-dimension
getStepsizeY() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get the physical size of a voxel (stepsize) in y-dimension
getStepsizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get the physical size of a voxel (stepsize) in y-dimension
getStepsizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the physical size of a voxel (stepsize) in z-dimension
getStepsizeZ() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get the physical size of a voxel (stepsize) in z-dimension
getStepsizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get the physical size of a voxel (stepsize) in z-dimension
getStomataCount() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves: Get number of stomata regions in set.
getString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBStringData
getSubdirectoryList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree: Get a list of all subdirectories in the root folder.
getSubtreeDirList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData: Collects the list of all sub-directories of this directory.
getSubtreeFileList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData: Collects the list of all files inside this directory and also inside all subdirectories.
getSuccessorSegment() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Get subsequent segment along contour.
getSum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
getSummary() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
getSurfaceImage() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: draw surfaces into an image with the surface ids as labels
getSurfaces() - Method in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
getSynthMask(SegmentationInitializer.SegmentationDimension) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Generate synthetic mask.
getT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getTable() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
getTable() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
getTableEntry(int) - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult: Returns entry in requested field as string representation.
getTableEntry(int) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
getTableEntry(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
getTableEntry(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
getTangentOrientation(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Returns the orientation of the tangent at point p on the ellipse.
getTargetImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Get the target image to which the regions are drawn, if one was specified.
getTargetImageType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getTgtNode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Get target node of the MTBGraphEdge.
getTheta() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Get coefficient to relate vessel radius and scale.
getThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get threshold to be applied to image.
getThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Get value of threshold.
getThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Get threshold.
getThresholdImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Get image for thresholding
getThresTH() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Get value of thresTH.
getTicks() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime: Declaration of native method for getting ticks.
getTile(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Returns tile with given indices.
getTileCenterX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Returns x-coordinate of tile center.
getTileCenterY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Returns x-coordinate of tile center.
getTileCols() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Returns number of tiles and colums, respectively, in x-dimension.
getTileCountX() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Get number of tiles in x-direction.
getTileCountY() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Get number of tiles in x-direction.
getTileRows() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Returns number of tiles and rows, respectively, in y-dimension.
getTitle() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the image's title
getTitle() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get title string
getTitle() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get title of underlying image
getTitleRunning(String) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Return a unique title for the copy of an image, i.e. a running number is appended/incremented.
getTotalDistances(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
getTotalLength() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Get total length.
getTotalNumberOfEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Get total number of edges for MTBGraphNode.
getTrack(short) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: Get track of target given by targetID up to current time, where targetID may be 0 to obtain the clutter observations (which do not form a track).
getTrackImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
getTrackReport() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
getTrajectories() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
getTrajectories() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
getTransferFunktion(MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization: Get the discrete transfer function for the histogram.
getTransformMatrix() - Method in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
getTransitionMatrices() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
getType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get MiToBo image type
getType() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get data type
getType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get underlying data type
getType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Returns the type of the curve.
getType() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Get input image type.
getType() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Get type of markers.
getTypeMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Return the maximum value that the current type can handle
getTypeMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Return the minimum value that the current type can handle
getTypeName(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Deprecated.
getU() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Get vector U of the field.
getUniqueClassIdentifier() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
getUniqueClassIdentifier() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
getUniqueName(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Generates a unique name for a new roi in the manager.
getUnitT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the unit of the t-dimension
getUnitT() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get the unit of the t-dimension
getUnitT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get the unit of the t-dimension
getUnitX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the unit of the x-dimension
getUnitX() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get the unit of the x-dimension
getUnitX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get the unit of the x-dimension
getUnitXY() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
getUnitXYZ() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
getUnitY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the unit of the y-dimension
getUnitY() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get the unit of the y-dimension
getUnitY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get the unit of the y-dimension
getUnitZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the unit of the z-dimension
getUnitZ() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get the unit of the z-dimension
getUnitZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get the unit of the z-dimension
getUpperBound() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools: Get upper bound of the normalization to range [lowerBound, upperBound].
getUserTime() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime: Declaration of native method for user time measurement.
getUseThresh() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Get adaptive thresholding tag.
getUWT() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Get the UWT coefficient images.
getV() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Get vector V of the field.
getValue(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get RGB value from the specified position.
getValue(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get RGB value from the specified position in the actual slice.
getValue(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
getValue() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData: Returns the double value.
getValue() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
getValue(NodeList, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
getValue(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper: Calculate approximated value for given parameter value.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance: Returns the distance value from the distance map at the given position.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient: Returns the negative absolute gradient value to the power of 2 (the external energy) at the given position.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D: Returns the value of the external energy at the given position.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity: Returns the value of the external energy at the given position.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Returns the value of the external energy at the given position.
getValue_norm(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Returns the value of the external energy at the given position on a normalizes image coordinates in range [width*scale, height*scale].
getValueAt(int, int) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
getValueB(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get blue value from the specified position.
getValueB(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get blue value from the specified position in the actual slice.
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the value of the 5D image at coordinate (x,y,z,t,c) as a Double
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the value of the current slice at coordinate (x,y,z) as an Double
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the value of the current slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Get the value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get the value of the 5D image at coordinate (x,y,z,t,c) as a Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get the value of the actual slice at coordinate (x,y) as a Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get the value of the 5D image at coordinate (x,y,z,t,c) as a Double
getValueG(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get green value from the specified position.
getValueG(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get green value from the specified position in the actual slice.
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the value of the 5D image at coordinate (x,y,z,t,c) as an Integer
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the value of the current z-stack coordinate (x,y,z) as an Integer
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the value of the current slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Get the value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Get the value of the 5D image at coordinate (x,y,z,t,c) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get the value of the 5D image at coordinate (x,y,z,t,c) as an Integer
getValuePotential(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Returns value of potential at specified position.
getValueR(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get red value from the specified position.
getValueR(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Get red value from the specified position in the actual slice.
getValues() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Get the double values of the given image.
getValueU(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Get value from vector U at position (x,y).
getValueV(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Get value from vector V at position (x,y).
getVariance() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
getVectorField() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Get the operation based 2D vector field.
getVectorField() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Get the resulting 2D vector field.
getVectorField() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Get calculated GVF vector field..
getVectorFieldImage() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Get the operation based 2D vector field image.
getVectorFieldImage() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Get the resulting 2D vector field image.
getVectorIndex(CellCntrMarker) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Returns the index of the given marker.
getVersion() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
getVersionProvider() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools: Returns version provider object.
getVisibilityMapHeight() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns height of the visibility map.
getVisibilityMapWidth() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns width of the visibility map.
getVisibilityMapXMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns maximal x coordinate represented in visibility map.
getVisibilityMapXMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns minimal x coordinate represented in visibility map.
getVisibilityMapYMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns maximal y coordinate represented in visibility map.
getVisibilityMapYMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Returns minimal y coordinate represented in visibility map.
getVolume() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Return the volume of the 3D region (number of points within the region).
getVolume() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution: Get volume of the hypercube where p(x) > 0
getVoronoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Returns set of snake polygons resulting from Voronoi tesselation.
getVoronoiImg() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile: Get voronoi tesselation image.
getVoronoiStack() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Get stack of voronoi tesselation images.
getVotesAdjacency(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
getVotesClutter(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
getVotesTarget(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Get weight of idx-th particle
getWeight(double, double) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Return edge weight for edge between given nodes.
getWeight(int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy: Returns the weight of the energy with given index.
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: Returns element i of the weight list.
getWeight(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
getWeight(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
getWeight(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Returns the pixel weight of position (x,y).
getWeight(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Returns the pixel weight of position (x,y,z).
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Returns element i of the weight list.
getWeight(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable: Returns element i of the weight list.
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable: Returns element i of the weight list.
getWeight(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
getWeight(PartitGraphNodeID, PartitGraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
getWeight(T, T) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix: Get weight of edge from nodeSrc to nodeTgt.
getWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
getWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Get particle weights
getWeights() - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy: Returns the list of weights.
getWeights() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: Returns the list of weights.
getWeights() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Returns the list of weights.
getWeights() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable: Returns the list of weights.
getWeights() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable: Returns the list of weights.
getWeightsSum() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Get sum of weights
getWidth() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D: Get the width associated with the segment.
getWidth() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Get skeleton graph image size in x direction.
getWidth() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Get image width.
getWidth() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Get image width.
getWidth() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Get image width.
getWidth() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Get image width.
getWidth() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Get width of level set function domain.
getWindowPosition() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Get the current window position
getWorkingImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Returns working image.
getWorkingImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
getWorkingImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
getWthImage() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Get white top-hat image.
getWthMaskSize() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Get mask size of white top-hat.
getX() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
getX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Return coordinate of x-dimension.
getX() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Get x-coordinate.
getX() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
getXMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Get the maximal x-coordinate of the domain of this border set.
getXMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Get the maximal x-coordinate of the domain of this contour set.
getXmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Returns maximal x coordinate of the domain.
getXmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
getXmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
getXmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
getXMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Get the minimal x-coordinate of the domain of this border set.
getXMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Get the minimal x-coordinate of the domain of this contour set.
getXmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Returns minimal x coordinate of the domain.
getXmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
getXmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
getXmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
getXML() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Get the XML file description string if one was available.
getXMTBImg() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Get the value channel image.
getXPos() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Get x-position of the node.
getXThresh() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: The Intensity/Brighntness/Value-Parameter (depending on the used input image type).
getXylemImage() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Return the Hue/Saturation/{Intensity|Brightness|Value}-MTBImage.
getXylemImage() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: Return the input xylem image.
getY() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
getY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Return coordinate of y-dimension.
getY() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Get y-coordinate.
getY() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
getYMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Get the maximal y-coordinate of the domain of this border set.
getYMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Get the maximal y-coordinate of the domain of this contour set.
getYmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Returns maximal x coordinate of the domain.
getYmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
getYmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
getYmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
getYMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Get the minimal y-coordinate of the domain of this border set.
getYMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Get the minimal y-coordinate of the domain of this contour set.
getYmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Returns minimal y coordinate of the domain.
getYmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
getYmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
getYmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
getYPos() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Get y-position of the node.
getZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
getZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Return coordinate of z-dimension.
getZ() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Get z-coordinate.
getZ() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
getZmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
getZmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
getZmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
getZmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
gif - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
GlobalContrastStretching - Class in de.unihalle.informatik.MiToBo.enhance: Global contrast stretching.
GlobalContrastStretching() - Constructor for class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching: Default constructor.
GlobalContrastStretching(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching: Constructor with default image.
gradField - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
GradientFieldCalculator2D - Class in de.unihalle.informatik.MiToBo.fields: Class to calculate a gradient vector field of a given image.
GradientFieldCalculator2D() - Constructor for class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Standard constructor.
GradientFieldCalculator2D(MTBImage, GradientFieldCalculator2D.GradientMode) - Constructor for class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Constructor.
GradientFieldCalculator2D.GradientMode - Enum in de.unihalle.informatik.MiToBo.fields: Provided calculation modes for calculation the gradient image.
GradientFieldNonMaxSuppression - Class in de.unihalle.informatik.MiToBo.fields: Non-Maximum-Suppression and (optional) hysteresis thresholding on gradient fields.
GradientFieldNonMaxSuppression() - Constructor for class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression: Standard constructor.
gradientMode - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: The used gradient mode for field calculation.
GradientMode() - Constructor for enum de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D.GradientMode
gradMagHeaviside(double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2D2PNonPDE: calculate the gradient magnitude of the foreward difference of the heavyside function corresponding to the level set for one pixel
gradMagHeaviside(double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DMPNonPDE: calculate the gradient magnitude of the foreward difference of the heavyside function corresponding to the level set for one pixel
gradMagHeaviside(double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE: calculate the gradient magnitude of the foreward difference of the heavyside function corresponding to the level set for one pixel
gradMagHeaviside(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE: calculate the gradient magnitude of the forward difference of the heaviside function corresponding to the level set for one voxel
gradMagHeaviside(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DMPNonPDE: Calculate the gradient magnitude of the foreard difference of the heavyside function corresponding to the level set for one voxel
gradMagHeaviside(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE: calculate the gradient magnitude of the foreward difference of the heavyside function corresponding to the level set for one voxel
graph - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
GraphNode(int, int) - Constructor for class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder.GraphNode: Default constructor.
GraphNodeID - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl: A graph node object to hold a nodeID as well as a subgraphID
GraphNodeID(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID: Constructor (subgraphID=0)
GraphNodeID(int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID: Constructor to assign the node to a subgraph
GraphvizWriter<T extends Comparable<?> & Comparator<?>> - Class in de.unihalle.informatik.MiToBo.io.files: Write graph to file using the DOT-language for visualization using graphviz tools.
GraphvizWriter() - Constructor for class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter: Empty constructor
GraphvizWriter(AdjacencyMatrix<T>, String) - Constructor for class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter: Constructor for specifying the graph by an adjacency matrix
GraphvizWriter(MTBGraph, String) - Constructor for class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter: Constructor for specifying the graph by MTBGraph
gratwanderung(int, int, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Function to travers ridges.
GrayscaleImageToHeatmap - Class in de.unihalle.informatik.MiToBo.visualization.colormappings: This operator converts a gray-scale image to a heat map image.
GrayscaleImageToHeatmap() - Constructor for class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Default constructor.
GrayscaleImageToHeatmap.OperationMode - Enum in de.unihalle.informatik.MiToBo.visualization.colormappings: Operation mode of the operator.
GrayscaleImageToHeatmap.OutOfRangeValuesHandlingMode - Enum in de.unihalle.informatik.MiToBo.visualization.colormappings: Available modes how to handle values out of range.
GrayscaleToGrayscaleMapping - Class in de.unihalle.informatik.MiToBo.visualization.colormappings: This operator transforms the intensity values of a gray-scale image according to a given intensity mapping.
GrayscaleToGrayscaleMapping() - Constructor for class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Default constructor.
GrayscaleToGrayscaleMapping.IgnoredValuesHandlingMode - Enum in de.unihalle.informatik.MiToBo.visualization.colormappings: Available modes how to handle ignored values.
GrayscaleToGrayscaleMapping.OperationMode - Enum in de.unihalle.informatik.MiToBo.visualization.colormappings: Operation mode of the operator.
grayValue - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
grayValue - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Gray value used, e.g., for mask or contour images.
GreedyGourmetPartitioning - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo: greedyGourmet graph partitioning algorithm following:
J.
GreedyGourmetPartitioning(MatchingAdjacencyMatrix, boolean, double) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning: Constructor.
green - Static variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Definition of green color.
GREEN_COMPONENT_INDEX - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
GroundtruthEvaluation - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation: Implementation of segmentation evaluation measures.
GroundtruthEvaluation() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Default constructor.
GroundtruthEvaluation(MTBImage, MTBImage, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Default constructor with parameters.
groundtruthObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
groundtruthToSampleTargetIDs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
GrowingMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingMode
growingRegion - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
GrowingRegion2D(MTBRegion2D, MTBImageByte, XylemGrower.Neighbourhood, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
grownRegionImage - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
grownRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: Resulting regions from growing.
grownRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Resulting regions from growing.
growRandomRegion2D(int, int, int, int, int, MTBRegion2D, Random) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Grow a 2D region adding the pixel specified and potentially grow further
growRegion() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D: Grow the region.
growthCones - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Neurite corresponding growth cone regions as MTBRegion2D objects.
GTC - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Check if you want to compute Recall and Precision
gtContours - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours: List of point-wise groundtruth contours.
gtContours - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: List of contours of groudtruth objects.
gtIDs - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Match list of set entries to original groundtruth labels.
gtIDs - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Match list of set entries to original groundtruth labels.
gtImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: Groundtruth labeling.
gtLabelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Preprocessed groundtruth label image with short pixel type.
gtLabelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Groundtruth labeling.
gtLabels - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: List of labels of groundtruth regions.
gtLabelsOrig - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Groundtruth labeling.
gtRegionLabels - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours: List of labels of groundtruth regions.
guiElements - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.
gvf - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D: The resulting gradient vector flow field.
GVFFieldCalculator2D - Class in de.unihalle.informatik.MiToBo.fields: Class to calculate a special 2D vector field, a Gradient Vector Flow Field (GVF) with its x- and y-flows from the given image.
GVFFieldCalculator2D() - Constructor for class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Standard constructor.
GVFFieldCalculator2D(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Constructor.

H

h - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter: Array of hue values.
h - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter: Hue of HSV space.
h - Variable in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
h(ArrayList<Point>, ArrayList<Point>) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_HausdorffDistance: This methods computes for all points in a contour the maximum minimal distance to an other contour.
H - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians: state-to-observation-space linear transform matrix
H - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
HaralickDirection() - Constructor for enum de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures.HaralickDirection
haralickMeasures - Variable in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult: Result values.
hasEnergies() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Check if energies are given.
hasEnergies() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
hasEnergies() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
hasForeign26Neighbor(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
hasForeign4Neighbor(short, short[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Check whether there is a different/foreign phase (then phase) in the 4-neighborhood as represented in the 8 neighborhood nbPhases.
hasForeign6Neighbor(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
hashCode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
hashtableToString(Hashtable<Integer, Vector<Double>>, String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
hashtableToString(Hashtable<Integer, Vector<Double>>, String, Hashtable<Integer, Integer>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
hasImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
hasNext() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
hasNext() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
hasNext() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
hasNext() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
hasNext() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelIndexIterator
hasNext() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
hasOneCC() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: Checks if the neighborhood represented in X has exactly one connected component of entries set to true using the neighborhood definition as as represented in the neighborhood arrays of the class.
HAU - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Check if you want to compute the Hausdorff-Distance
HAU() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_HausdorffDistance: This method is the implementation of the Hausdorff Distance
haveJNI - Static variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime: Were we able to load the JNI library?
HDomeTransform3D - Class in de.unihalle.informatik.MiToBo.morphology: H-dome transform in 3D (straightforward use with 2D-images).
HDomeTransform3D() - Constructor for class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D: Constructor
HDomeTransform3D(MTBImage, double) - Constructor for class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D: Constructor
head - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
header - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel: Header defines.
headerStrings - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Header defines.
height - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Height of the input image.
height - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Height of the input image.
height - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
height - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Image size in y-direction, given in pixel.
height - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Height of the binary neuron image.
height - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
height - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Height of the processed image.
height - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Skeleton image size in y-direction.
height - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Height of the image where the vector field comes from.
height - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Height of currently processed image.
height - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper: Height of reference image domain.
height - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Height of input label image.
height - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Height of the image.
height - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Size of the image and the calculated gvf field in y-direction.
height - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D: Height of the filter mask.
height - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D: Height of the filter mask.
height - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Height of the filter mask.
height - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
height - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Height of the given image.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Height of segmentation domain.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: Height of segmentation domain.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Image height.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Image height.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Height of label images.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Height of label images.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter: Input image height.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Height of the input image and levelset function.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Height of the input image.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Height of the given image for the energy.
helperArray - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: 2D array of first two levelset dimension used for visualization
highBound - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: upper boundary of the last bin
highContrast - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Highest grayscale value of the line.
highContrast - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Highest grayscale value of the line.
higherThresholdRatio - Static variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Factor to choose higher threshold in hysteresis thresholding automatically.
highQualityData - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Flag to enable extraction of data with highest accuracy.
histBins - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPs: Number of histogram bins.
histBins - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPsRIU: Number of histogram bins.
histBins - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Number of histogram bins.
histogram - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
Histogram() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
HistogramEqualization - Class in de.unihalle.informatik.MiToBo.enhance: Histogram linearization by entropy maximization.
HistogramEqualization() - Constructor for class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization: Default constructor.
HistogramEqualization(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization: Constructor with default image.
HistogramFrame(double[]) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.HistogramFrame
histoRegionSize - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Size of region for histogram binning.
hookPointsUpdated() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Function to update object state after setting new point list.
hookPointsUpdated() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Function to update object state after setting new point list.
hookPointsUpdated() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Function to update object state after setting new point list.
hsiInput - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter: Input HSI values.
HSIToRGBPixelConverter - Class in de.unihalle.informatik.MiToBo.color.conversion: Operator to convert a single HSI value to RGB.
HSIToRGBPixelConverter() - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter: Default constructor.
HSIToRGBPixelConverter(double[]) - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter: Constructor.
HSVToRGBArrayConverter - Class in de.unihalle.informatik.MiToBo.color.conversion: Class to convert a whole array of values from HSV color space to RGB.
HSVToRGBArrayConverter() - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter: Standard constructor.
HSVToRGBArrayConverter(double[], double[], double[]) - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter: Constructor to create a HSVconverter object
HSVToRGBPixelConverter - Class in de.unihalle.informatik.MiToBo.color.conversion: Class to convert values from HSV color space into other color spaces like RGB or so.
HSVToRGBPixelConverter() - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter: Standard constructor.
HSVToRGBPixelConverter(double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter: Constructor to create a HSVconverter object
HUE_COMPONENT_INDEX - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
HUE_UNDEFINED - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
hueMeanDegree - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
hueMTBImg - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Hue channel image.
hueThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: The hue threshold.
hueThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: The hue threshold.
hullImage - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
hybridGrayscaleReconstruct(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D: Implements the fast hybrid grayscale reconstruction algo of [Vincent93].
HyperStackParticleDetectorUWT2D - Class in de.unihalle.informatik.MiToBo.apps.particles2D: A particle detector that runs the ParticleDetectorUWT2D given as input (with all parameters set) over all slices of the input image for a given channel.
HyperStackParticleDetectorUWT2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
HyperStackParticleDetectorUWT2D(MTBImage, ParticleDetectorUWT2D, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
HysteresisThresholding - Class in de.unihalle.informatik.MiToBo.segmentation.thresholds: Hysteresis thresholding on gray-scale images.
HysteresisThresholding() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding: Standard constructor.

I

i - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.IntObject: Internal position counter.
ic - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Image canvas for displaying image and interacting.
iChannels - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Number of channels of the image.
iChannels - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Number of channels of working image.
iChannels - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Image channels.
iconData - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
iconData - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
iconLabel - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
iconLabel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
iconNoData - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
iconNoData - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
icov - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution: inverse covariance matrix
id - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
id - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Id of the region (uniqueness is not guaranteed nor checked!).
id - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: ID of the region (uniqueness is not guaranteed nor checked!)
id - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D: ID of the region (uniqueness is not guaranteed nor checked!)
ID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID: Target ID
identifiedRegions - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: List of validated plastid regions with stromules.
iDepth - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Depth of working image.
iDepth - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Depth of working image.
iDepth - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Depth of input image, i.e. dimension in z or third axis.
idImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Gray-scale image with IDs printed to regions.
idxUntitled - Static variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing: Index to number untitled images popped-up.
ignoreBorder - Variable in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction: Flag to indicate how the border should be handled.
ignoreButtonPress - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: Flag to ignore presses on either button.
ignoreButtonPress(boolean) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: Enable/disable buttons.
IgnoredValuesHandlingMode() - Constructor for enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping.IgnoredValuesHandlingMode
ignoredValuesMode - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Mode how to handle ignored values.
ignoreInvalidStackSpec - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
ignoreMask - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Optional binary mask of additional pixels to ignore.
ignoreMask - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Optional binary mask of additional pixels to ignore.
ignoreStructsAtBorder - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Flag to ignore structures along border.
ignoreStructsInNuclei - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Height of working image.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Height of working image.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Height of input image, i.e. dimension in y or second axis.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker: Height of the image to be generated.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Height of working image.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Image height.
IlluminationCorrection - Class in de.unihalle.informatik.MiToBo.enhance: This class corrects the uneven illumination (e.g. background gradient) of especially gray value bright filed or DIC images.
IlluminationCorrection() - Constructor for class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection: Standard constructor.
IlluminationCorrection(MTBImage, BasicMorphology, MTBImage.MTBImageType) - Constructor for class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection: Constructor to create a new IlluminationCorrection object.
image - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult: Reference to the image from which the segmentation data originates.
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Input image.
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient: The given input image to calculate the external energy from it.
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity: The given input image to calculate the external energy from it.
image - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter: Image to split.
image - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
image_channel - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Channel of the image that was processed.
IMAGE_FILE_PATH - Static variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Name of the image.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Name of the analyzed image.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Name of the analyzed image.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Name of the analyzed image.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel: Name of the analyzed image.
ImageArithmetics - Class in de.unihalle.informatik.MiToBo.math.images: Image arithmetics class for MTBImage objects.
ImageArithmetics() - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Create empty ImageArithmetics object.
ImageArithmetics(ImageArithmetics.ArithOp, MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Constructor for arithmetic operations considering two images.
ImageArithmetics(ImageArithmetics.ArithOp, MTBImage, double) - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Constructor for arithmetic operations considering one image and a constant.
ImageArithmetics.ArithOp - Enum in de.unihalle.informatik.MiToBo.math.images: Arithmetic operations:
ADD, SUB, MULT, DIV, MIN, MAX, AND, OR, ABS_DIFF require two input images,
ADD_CONST, MULT_CONST, DIV_CONST, POW_CONST require one input image and a constant
INV, ABS require one input image only
imageClasses - Static variable in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter: all supported classes besides RGB
imageClosed(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
imageClosed(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
ImageContrastReducer - Class in de.unihalle.informatik.MiToBo.tools.image: Contrast-reduction of images by reducing number of gray-scale values.
ImageContrastReducer() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer: Default constructor.
ImageContrastReducer.ResultValueMode - Enum in de.unihalle.informatik.MiToBo.tools.image: Modes for choosing result values.
ImageContrastReducer.TargetContrast - Enum in de.unihalle.informatik.MiToBo.tools.image: Available target contrast modes.
ImageConvert - Class in cmdTools.mtb_imagetools: Commandline tool to convert image formats and datatypes.
ImageConvert() - Constructor for class cmdTools.mtb_imagetools.ImageConvert
ImageConverter - Class in de.unihalle.informatik.MiToBo.tools.image: Plugin to convert images that are represented by MTBImage.
ImageConverter() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageConverter: Constructor.
ImageConverter(MTBImage, MTBImage.MTBImageType, boolean, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageConverter: Constructor
ImageDimensionReducer - Class in de.unihalle.informatik.MiToBo.tools.image: Operator to reduce image dimension by projecting multi-dimensional images along selected dimensions.
ImageDimensionReducer() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Constructor.
ImageDimensionReducer(MTBImage, boolean, boolean, boolean, boolean, boolean, ImageDimensionReducer.ReducerMethod) - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Constructor with arguments.
ImageDimensionReducer.IntObject - Class in de.unihalle.informatik.MiToBo.tools.image: Internal helper class for iterating over an image dimension.
ImageDimensionReducer.ReducerMethod - Enum in de.unihalle.informatik.MiToBo.tools.image: Methods for dimension reduction/projection.
imageDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Input image directory.
imageDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Input image directory.
imageDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Input image directory.
imageFiles - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Vector with all image files included in the experiment folder for detection.
ImageFilter - Class in de.unihalle.informatik.MiToBo.io.tools: Class to filter the files by a file chooser.
ImageFilter() - Constructor for class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
ImageFilter(String[]) - Constructor for class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
imageHeight - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Height of the images taking first image as reference.
imageHeight - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Height of the images taking first image as reference.
imageHeight - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Height of the images, taking first image as reference.
imageIndex - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
ImageIOUtils - Class in de.unihalle.informatik.MiToBo.io.tools: A class of utility functions used by the MiToBo's image-IO classes
ImageIOUtils() - Constructor for class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
ImageMaker(MTBSnake, int, int, int, String, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker: Default constructor.
imageNormalized - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient: Normalized version of input image used in calculations.
imageNormalized - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity: Normalized version of input image used in calculations.
imageOpened(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
imageOpened(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
ImagePlusInteractionFrame - Class in de.unihalle.informatik.MiToBo.core.imageJ: Adapter for GUI interactions with ImageJ's ImagePlus.
ImagePlusInteractionFrame(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame: Default constructor.
ImageReaderMTB - Class in de.unihalle.informatik.MiToBo.io.images: Image reader operator to create MTBImage or ImagePlus objects from image files while reading and restoring image history from corresponding history files (.mph).
ImageReaderMTB() - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
ImageReaderMTB(String) - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Constructor of an image reader instance by filename.
ImageReaderMTB.OutImageType - Enum in de.unihalle.informatik.MiToBo.io.images: Specifies the image object that is constructed by the reader
ImageReaderOptionsPane - Class in de.unihalle.informatik.MiToBo.gui: A panel for image reader options that is used as accessory in a JFileChooser
ImageReaderOptionsPane(JFileChooser) - Constructor for class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane: Constructor that will install this reader options panel to the specified JFileChooser
ImageReaderOptionsPane.FileOptionsRefresher - Class in de.unihalle.informatik.MiToBo.gui
images - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
images - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
images - Variable in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
imagesAsMasks - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: If flag is true, only masks are copied to result stack.
ImageShowButton(Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowButton: Constructor.
ImageShowPanel(MTBImageDataIOSwing.ImageShowButton, String) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowPanel: Constructor.
ImageStatistics - Class in de.unihalle.informatik.MiToBo.math.images: Class offering statistical calculations on objects of type MTBImage.
ImageStatistics() - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageStatistics: Default constructor.
ImageStatistics(MTBImage, ImageStatistics.StatValue) - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageStatistics: Constructor with image argument.
ImageStatistics.StatValue - Enum in de.unihalle.informatik.MiToBo.math.images: Statistical values that could be calculated.
ImageToTilesSplitter - Class in de.unihalle.informatik.MiToBo.tools.image: Operator to split an image into tiles and save them to disk.
ImageToTilesSplitter() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter: Empty constructor.
ImageType() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.ImageType
imageType - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Desired type of output image.
imageTypeIsOk(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
imageUpdated(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
imageUpdated(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
ImageValueModification() - Constructor for enum de.unihalle.informatik.MiToBo.tools.image.ImageValueTools.ImageValueModification
ImageValueTools - Class in de.unihalle.informatik.MiToBo.tools.image: An operator class for different simple operations on the values of an image like inversion, filling with a constant value, etc.
ImageValueTools() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
ImageValueTools(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools: Constructor.
ImageValueTools.ImageValueModification - Enum in de.unihalle.informatik.MiToBo.tools.image: Available image value modification methods.
imageWidth - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Width of the images taking first image as reference.
imageWidth - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Width of the images taking first image as reference.
imageWidth - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Width of the images, taking first image as reference.
ImageWriterMTB - Class in de.unihalle.informatik.MiToBo.io.images: Image writer operator to store MTBImage or ImagePlus to disk along with the image history (.mph) file.
ImageWriterMTB() - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
ImageWriterMTB(MTBImage, String) - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Image file output operator for MTBImage objects.
ImageWriterMTB(ImagePlus, String) - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Image file output operator for ImagePlus objects.
ImageWriterOptionsPane - Class in de.unihalle.informatik.MiToBo.gui: A panel for image writer options that is used as accessory in a JFileChooser
ImageWriterOptionsPane(JFileChooser) - Constructor for class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane: Constructor that will install this writer options panel to the specified JFileChooser
ImageXX - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
ImageXY - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
ImageYX - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
ImageYY - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
img - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame: Associated MiToBo image.
img - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE: Image to be segmented
img - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE: Image to be segmented
img - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE: Image to be segmented
img - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
ImgClose - Class in de.unihalle.informatik.MiToBo.morphology: This class implements morphological closing on 2D binary/grayscale images.
ImgClose() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgClose: Default constructor.
ImgClose(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgClose: Constructor.
ImgDilate - Class in de.unihalle.informatik.MiToBo.morphology: This class implements morphological dilation on 2D binary/grayscale images.
ImgDilate() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgDilate: Default constructor.
ImgDilate(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgDilate: Constructor.
ImgErode - Class in de.unihalle.informatik.MiToBo.morphology: This class implements morphological erosion on 2D binary/grayscale images.
ImgErode() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgErode: Default constructor.
ImgErode(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgErode: Constructor.
imgFile - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter: File from where to load the image to split.
ImgOpen - Class in de.unihalle.informatik.MiToBo.morphology: This class implements morphological opening on 2D binary/grayscale images.
ImgOpen() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgOpen: Default constructor.
ImgOpen(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgOpen: Constructor.
imgPlusRef - Variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox: ImagePlus object in container.
imgReadInfo(IFormatReader) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils: Create a string of image reading information
imgStatsOp - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Operator to calculate energy parameters, i.e., some statistical numbers on the regions of the segmentation.
imgStatsOp - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Operator to calculate energy parameters.
ImgThresh - Class in de.unihalle.informatik.MiToBo.segmentation.thresholds: Image thresholding operator with lower threshold (threshold and upper threshold (upperThreshold.
ImgThresh(MTBImage, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Constructor for thresholding using 255 as foreground and 0 as background value.
ImgThresh(MTBImage, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Constructor for thresholding using 'fgValue' as foreground and 'bgValue' as background value.
ImgThresh() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
ImgThreshNiblack - Class in de.unihalle.informatik.MiToBo.segmentation.thresholds: Image binarization based on local Niblack thresholding.
ImgThreshNiblack() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Default constructor.
ImgThreshNiblack(MTBImage, ImgThreshNiblack.Mode, double, double, int, int, double, MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Constructor.
ImgThreshNiblack.Mode - Enum in de.unihalle.informatik.MiToBo.segmentation.thresholds: Niblack processing mode.
ImgTophat - Class in de.unihalle.informatik.MiToBo.morphology: This class implements the tophat operator.
ImgTophat() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgTophat: Default constructor.
ImgTophat(MTBImage, ImgTophat.tophatMode, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgTophat: Constructor with parameters.
ImgTophat.tophatMode - Enum in de.unihalle.informatik.MiToBo.morphology: Available operating modes.
imgWriteInfo(String, IFormatWriter, int) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils: Create a string of image writing information
imType - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Image type.
imType - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker: Type of the image to be generated.
include - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
include - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
includeMask(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
inConst - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
inContour - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter: Input contour.
inContours - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Set of contours to compute curvatures for
incrPositionC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Increment the window's position by 1 in the c-dimension
incrPositionC(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Increment the window's position by 'increment' in the c-dimension
incrPositionT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Increment the window's position by 1 in the t-dimension
incrPositionT(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Increment the window's position by 'increment' in the t-dimension
incrPositionX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Increment the window's position by 1 in the x-dimension
incrPositionX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Increment the window's position by 'increment' in the x-dimension
incrPositionY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Increment the window's position by 1 in the y-dimension
incrPositionY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Increment the window's position by 'increment' in the y-dimension
incrPositionZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Increment the window's position by 1 in the z-dimension
incrPositionZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Increment the window's position by 'increment' in the z-dimension
inData - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper: Input data.
indentationSegs - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: List of indentation segments along the contour.
IndependentlyEvaluatableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for densities p(X) with independent variables in X, that can be evaluated for each element in the realization x of its random variable X.
IndependentSamplingDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for densities with independent variables, where components of a sample can be drawn independently.
index - Variable in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
indexOfLowestPoint(Point2D.Double[]) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
indexOfRightmostPoint(Point2D.Double[], Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
indexR1 - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal: Channel index of code image for R = 1.
indexR2 - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal: Channel index of code image for R = 2.
indexR3 - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal: Channel index of code image for R = 3.
inDir - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Input directory where to find the images to process.
inDir - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Input directory where to find the images to process in batch mode.
inDir - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Input directory.
inDir - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Input directory.
individually - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Process each component individually (only active if ConvexHullExtraction.inType is InputType.IMAGE).
inEdges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Vector of incoming edges of the MTBGraphNode.
inf - Static variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
inFile - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Input file name.
InflectionPoint(double, double, MorphologyAnalyzer2DInProData.SegmentType) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InflectionPoint: Default constructor.
inflectionPoints - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: List of inflection points along the contour.
info - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: Information about this set of line segments.
info - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Information about this region set
inHisto - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu: Input histogram.
inImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker: Optional input image to be used for drawing.
inImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Input image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Input grayscale image/stack to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Multi-channel input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Single-layer input image to be processed.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Reference to original image, for internal use only
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Binary input image to be analyzed.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Multi-channel input image to be processed.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT: Gray-scale input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Gray-scale input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
inImg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
inImg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching: Input grayscale image.
inImg - Variable in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization: Input image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Input image to be processed.
inImg - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
inImg - Variable in class de.unihalle.informatik.MiToBo.features.FeatureCalculator: Input image to calculate features for.
inImg - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Label image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Input image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
inImg - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
inImg - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Input image to be processed.
inImg - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Input gray-scale image.
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: (Binary) Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgClose
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgErode
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor: Binary input image, pixels with value 0 are interpreted as background.
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.WatershedBinary: Binary input image to segment.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Image to work on.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Image to work on.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Input image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter: Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Input image to be segmented.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu: Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding: Image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer: Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Multi-dimensional input image or input stack.
inImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Input image where to draw the ellipse into.
inImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
inImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D: Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage: Input image to which the string is to be drawn.
inImg1 - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
inImg2 - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
inImgOrig - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Input image to process.
init() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Initialization method.
init() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Initialize detector.
init() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Initialization method.
init() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Initialization method.
init() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Initializes the operator, i.e. allocates memory.
init() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Method to properly initialize instances of this class.
init() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Method to properly initialize instances of this class.
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE: Initialize the energy object.
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE: Initialize the energy object.
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Initialization routine which is called once before the energy is actually used.
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2P4NNonPDE: Here potentially anisotropic grids may be reflected setting weights accordingly
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE: Initialize the energy object.
init(MTBSnakeEnergyCD_KassCurvature) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt: Initialize the updater according to associated energy object.
init(MTBSnakeEnergyCD_KassCurvature) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
init(MTBSnakeEnergyCD_KassCurvature) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
init(MTBSnakeEnergyCD_KassLength) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt: Initialize the updater according to associated energy object.
init(MTBSnakeEnergyCD_KassLength) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
init(MTBSnakeEnergyCD_KassLength) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
init(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
init(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone
init(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner
init(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate: Initializing routine which is called once before the gamma adaptation is actually used.
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination: Initializing routine which is called once before the termination is actually used.
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
initAlpha - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt: Initial alpha value of the internal Kass energy.
initArrayRI(int) - Static method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs: Initializes the array with rotation invariant and uniform codes.
initArrayRIU(int) - Static method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs: Initializes the array with rotation invariant and uniform codes.
initBeta - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt: Initial beta value of the Kass curvature energy.
initBinImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
initEnergy(LevelsetSolverDerivatives) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
initEnergy(LevelsetSolverDerivatives) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
initEnergy(LevelsetSolverDerivatives) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
initEnergy(LevelsetSolverDerivatives) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable: Initializes the energy object according to given solver settings.
initEnergy(SnakeOptimizerCoupled) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
initEnergy(SnakeOptimizerCoupled) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
initEnergy(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable: Init routine which is called once before the energy is actually used.
initEnergy(SnakeOptimizerCoupled) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCoupled: Init routine which is called once before the energy is actually used.
initEnergy(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable: Init routine which is called once before the energy is actually used.
initFromDirectory() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree: Builds the directory tree by initiating the (recursive) parse procedure.
initFromLabels(MTBImage, MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Helper for constructors from a label image.
initGenerator - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver: Operator to generate initialization for the level set function.
initialGammas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Initial step size in snake optimization.
initialize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: initialize histogram, i.e. determine smallest non empty bin, largest non
empty bin, number of histogram entries and sum of the histogram
initialSegmentation - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Initial segmentation of xylem regions.
initialSegmentation - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver: Initial segmentation for initializing level set function.
initialSegmentationOut - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: Initial segmentation of xylem regions computed of supplied
initialSegmentPoints - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Initial border points of the segment (before any shift takes place).
initialSigmaOneHalve - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Flag to use initial sigma = 0.5 for the wavelet transform
initialSkelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Intermediate result: initial contour skeleton.
initialSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Initial snakes for cells, e.g. nuclei contours.
initialSnakes - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Set of initial snake contours.
initLabelImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
initLevelset(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Helper to initialize a two phase level set function of size as given by invalidImg with a circle/sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.
initLevelset(MTBImage, int, MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Initialize a two phase level set function by thresholding an image.
initLS() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Construct an initial level set function.
initMainFrame() - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Initialize the main window on opening the first image.
initMask - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
initNeighbors() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2D: This initializes all relevant arrays containing information on neighbors where maxDist defines the neighborhood, e.g.
initNewTab(ALDGrappaWorkbenchGraph) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench
initNodeNames() - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
initOperator() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Initial setip of the operator.
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Initializes the optimizer.
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Initializes the optimizer.
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy: Initializes the optimizer.
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Initializes the optimizer.
initReader() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Initialize the reader (this method is called in the constructor)
initRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
initReloadedTab(mxGraph, ALDWorkflow) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench
initReloadedWorkflow(mxGraph, ALDWorkflow) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench
initSegImageByte - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: The resulting binary image after the initial segmentation.
initSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver: Runs initializer to calculate initial segmentation.
initSolver() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Create a parameter object and set/initialize all objects.
initWorkbench() - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaFrame
inLabelImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
inMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
inModes - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
inner - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Set of inner borders if available.
innerContourLengthMin - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Minimum number of pixels a inner contour must have (length of the contour).
InProContourSegment() - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
inProDetails - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Vector with detailed result data on indentations and protrusions.
inputArray - Variable in class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D: Input data array.
inputArray - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: Input array to visualize.
inputConts - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet: Set of contours of type MTBContour2D to draw.
inputData - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
inputDir - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Define detector parameters.
inputDir - Variable in class de.unihalle.informatik.MiToBo.io.importer.GetMTBContour2DSetFromXSVFiles: Input directory from where to read the xSV files.
inputDir - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Image directory to process.
inputEntropy - Variable in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization: Initial Shannon entropy of the input image.
inputImage - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Multichannel fluorescence image of the labeled neuron.
inputImage - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
inputImage - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
inputImage - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Input image to process.
inputImage - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
inputImage - Variable in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
inputImage - Variable in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
inputImage - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
inputImage - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: The input image to get the gradient values and differences.
inputImage - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: The input image as base for the GVF field calculation.
inputImage - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
inputImage - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Input image to process.
inputImage - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
inputImage - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Binary input image.
inputImage - Variable in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
inputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: (Optional) input image where the borders should be extracted from.
inputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: The binary input image where the contours should be calculated from.
inputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Input image to label.
inputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
inputImage - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
inputImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet: Input image into which the contours are to be drawn.
inputImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet: Input image into which the polygons are to be drawn.
inputImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
inputImagePlus - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
inputImages - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Input images.
inputImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor: Input skeleton image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D: Input image to be processed.
inputImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos: Input image to be processed.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D: Input image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Input image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D: Input image to be processed.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Input image to be processed.
inputImg - Variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor: Input skeleton image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver: Image to segment.
inputImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
inputImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
inputImg - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Input image.
inputImg - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Input image.
InputMode() - Constructor for enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.InputMode
InputMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.InputMode
inputMTBImage - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
inputMTBImageRGB - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Input Image.
inputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
inputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
inputPolys - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet: Set of polygons of type MTBPolygon2D to draw.
inputRegExp - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Optional file filter.
inputRegions - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Optional set of pre-segmented input regions.
inputRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: (Optional) region set where the borders should be extracted from.
inputRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: The input regions where the contours should be calculated from.
inputRegions - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Set of regions to draw.
inputSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner
inputTreelines - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Input treelines to be improved and updated.
InputType() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction.InputType
InputType() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu.InputType
inputTypeChanged() - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Callback routine to change parameters on change of input type.
inputTypeChanged() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu: Callback routine to change parameters on change of input type.
inRange - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Dynamic range of image intensities.
inRegion - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter: Input region.
inRegions - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Input image to process.
inRegions - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
inRegions - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Set of input regions.
inRegs - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
insertData(Vector<Object[]>) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Appends a set of results to the table, i.e. adds a new row at the end.
insertState(Matrix, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState: Insert an additional state
insertState(Matrix, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
inSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker: Input snake.
inSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker: Input snake.
instance - Static variable in class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon: Singleton reference.
int2Color(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Transforms integer value to Color object.
IntegrableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for distributions with distribution functions that can be evaluated for each realization x of its random variable X.
IntensityAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
IntensityAnalyzer(MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
intensityImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
IntensityNormalizationMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.IntensityNormalizationMode
intermediateLS - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
intermediateLS - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
intermediatePhiColorImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Color image to visualize intermediate segmentation results.
intermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: List of intermediate result segmentations.
intermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Set of intermediate segmentation results, required for stack generation.
intermediateResultSamplingRate - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
intermediateResultStack - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
internalOutputDir - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Internal variable of output dir (to avoid modifying parameter).
IntersectionPoint2D(double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D.IntersectionPoint2D: Default constructor.
intImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
intNormMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Mode for normalizing image intensities.
IntObject() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.IntObject: Constructor.
intReport - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
intReport - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
inType - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Input type.
inType - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu: Input type.
inv(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Inverts the image.
inv(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Invert the image.
INVALID_PHASE - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Level set function value to represent invalid pixels
invalidColor - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
invalidImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
invalidImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
invalidTilesNum - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult: Number of invalid, i.e. background tiles.
inverseATrousDWT(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
inverseATrousDWT(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Inverse a trous DWT
inverseDifferenceMoment - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
invert() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement: inverts the values of the structuring element
invert(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
invertGroundtrouth - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Flag to invert ground-truth image prior to evaluation.
invertImage(MTBImage, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools: Invert the specified image.
invertInputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Flag to invert input image.
invertMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D: Flag to invert filter mask.
invertMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Flag to invert filter mask.
invertMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D: Flag to invert filter mask.
invertMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Flag to invert filter mask.
invertPixelValues - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: If true image values are inverted, i.e., the algorithm seeks to find a path along bright pixels.
invisibleRegionSet - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
invokeLaterRepaint(ImageReaderOptionsPane) - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
ioPanel - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel: Swing component to be integrated in GUI.
iRead - Static variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Operator for reading image files from disk.
isActive - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Flag to indicate if marker is active, by default true.
isActive() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Check if marker is active.
isAppliedComponentwise() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Return operator mode.
isBGOriginalValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Test if background pixels keep their original pixel values
isCellEditable(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel
isCellEditable(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow.MTBSet_SnkEnergyPDEGUITableModel
isClockwiseOriented(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper: Checks if polygon is oriented counter-clockwise.
isClosed - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Indicates if the polygon is closed or not.
isClosed() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Returns true if the polygon forms a closed polygon.
isConvertableToNumericalData() - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult: Indicates if result data can be 'condensed' to numerical values, e.g., for visualization purposes.
isConvertableToNumericalData() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
isConvertableToNumericalData() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
isConvertableToNumericalData() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
isConvex() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Check if polygon is convex.
isConvex(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper: Checks if a polygon is convex.
isCounterClockwiseOriented(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper: Checks if polygon is oriented counter-clockwise.
isDirected() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Directed or undirected graph?
isDirected() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
isDirected() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix: Returns true if graph has directed edges, false if undirected
isEmpty() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Returns true if this collection contains no elements.
isEmpty() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet: Returns true if this collection contains no elements.
isFGOriginalValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Test if foreground pixels keep their original pixel values
isForwardTransform() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Test if parameter object is set to (forward) transform (image to wavelet)
isFurther(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
isHorizontal - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
isHorizontal - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
isHorizontal - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
isHueUndefined(float) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Return true if the hue channel is undefined which is true is saturation is zero or undefined which in turn is encoded as zero.
isHueUndefined(int) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Return true if the hue channel is undefined which is true is saturation is zero or undefined which in turn is encoded as zero.
isInverseTransform() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Test if parameter object is set to Inverse Transform (wavelet to image)
iSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Total area/volume of working image.
isLess(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
isMeanFree - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Flag for indicating if input data is already mean-free.
isOrderedClockwise() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Check if points are ordered clockwise.
isOrderedCounterClockwise() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Check if points are ordered counter-clockwise.
isotropicCalcs - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures: Flag for isotropic calculations.
isotropicCalcs - Variable in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures: Flag for isotropic calculations.
isRegionBinaryMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Check for region input mode.
isRegistered(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess: Checks if an object is registered in the database.
isRegisteredImageBox(Object) - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess: Checks if the given image object is already registered.
isSaturationUndefined(float) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Return true if the saturation channel is undefined which is true if the x channel is zero.
isSaturationUndefined(int) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Return true if the saturation channel is undefined which is true if the x channel is zero.
isScaleValues() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter: Get flag if values are scaled to match the range of output type values if necessary
isSimple() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Check if polygon is simple, i.e. has no self-overlaps.
isSimple(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper: Checks if a polygon is simple.
isValid(MTBImage, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: returns true, if pixel/voxel is valid.
isValidType(MTBImage.MTBImageType) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Deprecated.
isVerbose() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
isVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
isVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
isVisible(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: True, if position (x,y) is visible.
isVisible(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: True, if position (x,y,z) is visible.
isVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: is this pixel visible?
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
isVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Get visibility of a certain pixel position.
itCounter - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Iteration counter.
itemStateChanged(ItemEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
iteration - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Iteration counter.
iterationsPerSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Number of iterations done for each snake.
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
iterator() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: Returns a iterator for the coordinatesNeighbors in the order as defined
iteratorOffsets() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: Returns a iterator for the pixelOffsets in the order as defined
iTimeDim - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Time dimensionality of input image, i.e. dimension in t or time line.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Width of working image.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Width of working image.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Width of input image, i.e. dimension in x or first axis.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker: Width of the image to be generated.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Width of working image.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Image width.

J

jarvisMarch(Point2D.Double[]) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Jarvis march convex hull computation
JComboBoxImage(String, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage: Default constructor.
jfc - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
jfc - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
JFeatureLibLBPAdapter - Class in de.unihalle.informatik.MiToBo.features.texture.lbp: Adapter for JFeatureLib's Local Binary Patterns.
JFeatureLibLBPAdapter() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapter: Default constructor.
JFeatureLibLBPAdapterRIU - Class in de.unihalle.informatik.MiToBo.features.texture.lbp: Implementation of rotation invariant uniform LBPs.
JFeatureLibLBPAdapterRIU(int) - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapterRIU: Default constructor.
Jmax - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Maximum scale to consider.
Jmax - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT: Maximum scale to consider.
Jmax - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Jmin - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Minimal scale to consider.
Jmin - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT: Minimal scale to consider.
jMode - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Mode for joining results from different orientations.
join(MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Join a region with this region.
JoinMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer.JoinMode
jpeg - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
jpg - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
junitTest - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Internal flag for interrupting recursive calls in unit testing.

K

k - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
k - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Used only for MODIFIED_FREEMAN_DAVIS
K_MIN - Static variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: in length of vector k as suggested by H.Freeman and L.S.Davis
keepLargestCC(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: remove all but the largest connected component with label from
KERNEL_TYPE() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.KERNEL_TYPE
kernelImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
kernelMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Internal helper mask to mark valid/invalid kernel elements.
kernelNormalization - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
kernelOrigin - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
KernelPart() - Constructor for enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.KernelPart
kernels - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
kernelSize - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Size of the (squared) kernel window.
kernelTrunctation - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
keyPressed(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
keyPressed(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
keyReleased(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
keyReleased(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
keyTyped(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
keyTyped(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
kLower - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Used only for BEUS_TIU
KMeans - Class in de.unihalle.informatik.MiToBo.clustering: Clustering of (feature) vectors with k-means based on Weka library.
KMeans() - Constructor for class de.unihalle.informatik.MiToBo.clustering.KMeans: Default constructor.
kNearestObs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN: Stores for each observation the k-nearest observations that will be associated after the corresponding observation.
kNearestObservations(int, double) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN: Get the (k) nearest observations for each observation in this.Z, i.e. for each observation z_m all following observations z_{m:M} are sorted by Euklidean distance and stored in an array.
kPart - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Variable to configure which part of kernel mask is calculated.
kUpper - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Used only for BEUS_TIU
kurtosis(Vector<Double>, double, double) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
kurtosisFiltering(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter

L

L - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
label(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
LabelAreasToRegions - Class in de.unihalle.informatik.MiToBo.segmentation.regions.labeling
LabelAreasToRegions() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelAreasToRegions
labelComponents(MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Sequential component labeling
labelComponentsOfImage(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Label a MTBImage.
LabelComponentsSequential - Class in de.unihalle.informatik.MiToBo.segmentation.regions.labeling: Sequential component labeling for binarized 2D images to find connected components.
LabelComponentsSequential() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Constructor.
LabelComponentsSequential(MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Constructor.
LABELHEIGHT - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
labelImage - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Label mask.
labelImage - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Gray-scale label image of nuclei regions.
labelImage(MTBImage, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
labelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
labelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage: Input image.
labelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Grayscale image of regions, gray values are identical to IDs.
labelImageColor - Variable in class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter: Colored label image.
LabelImageConverter - Class in de.unihalle.informatik.MiToBo.segmentation.helpers: Converts (pseudo-) colored RGB labels to unique gray-scale labels.
LabelImageConverter() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter: Default constructor.
LabelImageConverter(MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter: Default constructor with parameters.
LabelImageEditor - Class in de.unihalle.informatik.MiToBo.tools.interactive: A small interactive tool for editing label images by mouse-clicks.
LabelImageEditor() - Constructor for class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Default constructor.
labelImageGray - Variable in class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter: Output gray-scale image.
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D: Binary nuclei image to be processed.
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos: Input image to process.
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
labelImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
labelImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper: Input label image.
labelImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
labelImg - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
labelInside - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Marker for label of enclosed area.
labelIO - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to read a label image.
labelListGT - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: List of groundtruth region labels.
labelListSG - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: List of labels found in segmentation.
labelNeighbors(MTBImage, MTBImage, int, int, double, double) - Static method in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression: Function for recursive labeling of contour pixels.
labelNeighbors(MTBImage, MTBImage, boolean[][], int, int, double, double) - Static method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding: Function for recursive labeling of foreground pixels.
labelResult - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
labels - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
labels - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
labelSetGT - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Set of available groundtruth labels.
labelsetGT - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Set of available groundtruth labels.
labelSetSG - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Set of available segmentation labels.
labelsetSG - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Set of available segmentation labels.
LABELWIDTH - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
lambda - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
lambda - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution: mean=variance of the distribution
lambda_in - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Weighting factors for inner region fit, one for each channel.
lambda_out - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Weighting factors for outer region fit, one for each channel.
lambdaArray - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE: An array of lambda values to be set in this energy object during initialization, i.e. the init() method.
lambdaArray - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE: An array of lambda values to be set in this energy object during initialization, i.e. the init() method.
lambdaBg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE: Lambda for background
lambdaBg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE: Lambda for background
lambdaBirth - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
lambdaBirth - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
lambdaClutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
lambdaClutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
lambdaDeath - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
lambdaDeath - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
lambdaFg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE: Lambda for foreground
lambdaFg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE: Lambda for foreground
lambdaForOptimization - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE: array to hold lambdas of phases, starting with MTBLevelsetMembership.BG_PHASE
largestNonEmptyBin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: largest intensity value contained in the input image
lastDir - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel: For convenience: always open last directory for saving.
lastDirectory - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel: Last directory selected by user.
lastDirectory - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel: Last directory selected by user.
lastDirectory - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Last directory visited, initially it's user's home.
lastFile - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel: Last file selected by user.
lastFile - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel: Last file selected by user.
lastFile - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Last selected file.
lastLabel - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Stores the last clicked label for transfer in memory mode.
lastM - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Number of observations in last call of drawSample()
lastN - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Number of targets in last call of drawSample()
lastPathPoint - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Local helper variable in drawing new boundaries, stores last point of current path.
lastProcessor - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Reference to last processor before last action.
lastSample - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Last sample that was sampled
layer - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Layer where the node is located.
LayerSubset() - Constructor for enum de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator.LayerSubset
LE(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors: This method implements the localization error.
leaveOneOutCrossValidation() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer: leave-one-out cross validation, i.e. iteratively one sample is taken as test
sample whereas all others are used for training
leftBorderPoint - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Left boundary point of segment after potential shifts.
leftBorderPointPosOnContour - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Index of left boundary point of segment after potential shifts.
leftOutlierFraction - Variable in class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching: Fraction of outlier pixels at left histogram margin.
length - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Expected length of vessel segments.
lengthEnergy - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
lengths - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
lengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
letNewbornTargetIDsStartFrom(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Specify the starting target-ID for newborn targets
letTargetsDie() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter: Let targets die randomly using the specified distribution of target death and the internal random generator.
LevelsetIterator() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIterator
LevelsetIteratorContourPoints() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
LevelsetIteratorScan() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
LevelsetSegmentationNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Operator intended as user interface for level set segmentation using nonPDE optimization and optionally topology preserving.
LevelsetSegmentationNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Default constructor.
LevelsetSolveNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Implements a level set solver which may optionally perserve the topology using non PDE optimization.
LevelsetSolveNonPDE(MTBGenericEnergyNonPDE, MTBLevelsetMembership, int, int, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Constructor.
LevelsetSolveNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Constructor
LevelsetSolveNonPDE.CoordInt3D - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Just to hold 3D coordinate and nothing else
LevelsetSolveNonPDE.LevelsetIterator - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Abstract class for iterators of pixels/voxels of the level set function.
LevelsetSolveNonPDE.LevelsetIteratorContourPoints - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Iterator for all contour pixels/voxels of the level set function excluding invalid pixels/voxels.
LevelsetSolveNonPDE.LevelsetIteratorScan - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Iterator for all pixels/voxels of the level set function in scanline fashion excluding invalid pixels/voxels.
LevelsetSolver - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core: Generic super class for level set solvers.
LevelsetSolver() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver: Default constructor.
LevelsetSolverDerivatives - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core: Level set solver using variational calculus.
LevelsetSolverDerivatives() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives: Default constructor.
LevelsetSolverPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver: Solver for level set segmentation problems based on PDEs.
LevelsetSolverPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Default constructor.
LevelsetSolverPDE.VelocityExpansionMode - Enum in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver: Available modes for expanding zero level velocities.
lif - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
limit - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
line() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine: Draw line into image.
LinearFilter - Class in de.unihalle.informatik.MiToBo.filters.linear: Generic linear filter operation class
LinearFilter() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Empty constructor
LinearFilter(MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Constructor
LinearFilter(MTBImage, MTBImage, int[], boolean, MTBImageWindow.BoundaryPadding) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Constructor
LinearTransformGaussNoise - Class in de.unihalle.informatik.MiToBo.math: A linear transform with additive Gaussian noise.
LinearTransformGaussNoise(Matrix, Matrix, Random) - Constructor for class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
lineSegmentSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: The set of line segments.
lineWidth - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Line width.
lineWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Line width.
LinkAdjacentComponents(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Function for linking adjacent components/regions in a binary image.
LinkAdjacentPixels(MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Function for linking adjacent pixels in a binary image.
linkageMode - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: The algorithm we use to link new pixels to the region.
linkageMode - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: The algorithm we use to link new pixels to the region.
llimits - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
LobeTypes() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.LobeTypes
localBinaryPatternHist - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult: Result values.
LocallyAdaptiveContrastEnhancement - Class in de.unihalle.informatik.MiToBo.enhance: This class implements contrast enhancement for microscopy images.
LocallyAdaptiveContrastEnhancement() - Constructor for class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Default constructor.
LocallyAdaptiveContrastEnhancement(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Constructor with given image.
LocallyAdaptiveContrastEnhancement(MTBImage, double, int) - Constructor for class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Constructor with given image and parameters.
localVersion - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile: Local version information.
localXThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
LOG - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution: Tells if the distribution is internally represented by the natural logarithm of the probability values
log_p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
log_p(Integer) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
log_p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
log_p(Integer) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
log_p - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
log_p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
log_p(T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.LogEvaluatableDistribution: Evaluate natural logarithm of p(X) at location x. log(P(X=x))
log_p(T, int) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.LogIndependentlyEvaluatableDistribution: Evaluate log(p_i(X)) at x_i
log_p(AbstractMultiState<S>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
log_p(AbstractMultiState<S>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep: Evaluate the density independently for observation i in Z conditional on state j in X
log_p(AbstractMultiState<S>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep: Evaluate the density independently for observation i in Z conditional on state i in X
log_p(AbstractMultiState<S>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
log_p(DataAssociation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: This method is here only valid for the latest DataAssociation sampled with drawSample().
log_p - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
log_p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
log_p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
log_p(AbstractMultiState<T>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
log_p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
log_p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
log_p(AbstractMultiState<T>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
log_pzc - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution: storage for the log likelihood values of the observations for possible associations to avoid recomputation
logarithmize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: calculate the logarithmic (base e) histogram; entries smaller than one become zero!
logBinom - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Binomial distribution of number of observations associated to existing targets
LogEvaluatableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for distributions that can be evaluated for each realization x of its random variable X.
logfac - Variable in class de.unihalle.informatik.MiToBo.math.LogFaculty: array to store log(0!)
logFac - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN: An object to compute and store log(n!)
logfactor - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution: log of the normalization factor
LogFaculty - Class in de.unihalle.informatik.MiToBo.math: Class to compute the logarithm of the faculty of an integer n.
LogFaculty(int) - Constructor for class de.unihalle.informatik.MiToBo.math.LogFaculty: Constructor to precompute log(0!)
LogIndependentlyEvaluatableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for densities p(X) with independent variables in X, that can be evaluated (natural logarithm) for each element in the realization x of its random variable X.
logMuValues - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: (log) values of mu to avoid recomputation
logNuValues - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: (log) values of nu to avoid recomputation
logp(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
logP_C - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: (log) probability of the current set of association variables given observations and previous associations
logP_Ccond - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: The probability of the association set of any time step represented by this sample conditional on all previous associations in this sample and all observations up to the specific time step: P(C^t | C^{1:t-1}, Z^{1,t}) for all t
logP_Cjoint - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: The joint probability of the association sets of all time steps represented by this sample conditional on all observations: P(C^{1-t} | Z^{1,t})
logP_MN - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: (log) propability of M observations given N existing targets and the current model configuration
logPofRegion(MTBRegion2D, MTBImage, MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
LogProbabilityDensityFunction - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for multivariate distributions that allow evaluation of the natural logarithm of their probability density function.
LogProbabilityMassFunction - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for univariate distributions based on log-probability mass functions
logSumP(double, double) - Static method in class de.unihalle.informatik.MiToBo.math.MathX: Natural logarithm of the sum of two values P1 and P2 when only their natural logarithms log(P1) and log(P2) are given.
longestPathLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
lowBound - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: lower boundary of the first bin.
lowContrast - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Lowest grayscale value of the line.
lowContrast - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Lowest grayscale value of the line.
lowerBound - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
lowerThresh - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Lower threshold for filter responses.

M

M - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution: number of observations
m - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
m - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
m1 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
m2 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
m_currentC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: current c-coordinate, for 3D only access functions
m_currentSliceIdx - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Index of the current slice.
m_currentT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: current t-coordinate, for 3D only access functions
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: reference to the ImagePlus pixel data
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: image data
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: reference to the ImagePlus pixel data
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: image data
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: reference to the ImagePlus pixel data
m_dataB - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: reference to the ImagePlus pixel data (blue channel)
m_dataG - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: reference to the ImagePlus pixel data (green channel)
m_dataR - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: reference to the ImagePlus pixel data (red channel)
m_height - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Height of input image.
m_idx - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: index of the minimum, median or maximum element in the sorted array
m_img - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: the underlying ImagePlus object
m_imgB - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: reference to the red channel MTBImage
m_imgG - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: reference to the red channel MTBImage
m_imgR - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: reference to the red channel MTBImage
m_imgStack - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: reference to the ImageStack object of the underlying ImagePlus object
m_impulator - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: source image on which the window is applied
m_labelImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Temporary label image.
m_level - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D: Tree level (level identifier).
M_max - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Maximum number of observations in the time series
m_padMode - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: padding mode for nonexistent values (outside the underlying image), see static finals
m_posC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: current c-position of the window in the source image
m_posT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: current t-position of the window in the source image
m_posX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: current x-position of the window in the source image
m_posY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: current y-position of the window in the source image
m_posZ - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: current z-position of the window in the source image
m_rC - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Radius of the median in the corresponding dimension.
m_reg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D: 2D region object.
m_rT - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Radius of the median in the corresponding dimension.
m_rX - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Radius of the median in the corresponding dimension.
m_rY - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Radius of the median in the corresponding dimension.
m_rZ - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Radius of the median in the corresponding dimension.
m_sigmaScales - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: noise sigma scale factors for different wavelet scales
m_sizeC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: size of c-dimension
m_sizeC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: size of the window in c-dimension
m_sizeC - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Size of the dimensions, size of the real stack.
m_sizeStack - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: stacksize
m_sizeT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: size of t-dimension
m_sizeT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: size of the window in t-dimension
m_sizeT - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Size of the dimensions, size of the real stack.
m_sizeX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: size of x-dimension
m_sizeX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: size of the window in x-dimension
m_sizeX - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Size of the dimensions, size of the real stack.
m_sizeY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: size of y-dimension
m_sizeY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: size of the window in y-dimension
m_sizeY - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Size of the dimensions, size of the real stack.
m_sizeZ - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: size of z-dimension
m_sizeZ - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: size of the window in z-dimension
m_sizeZ - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Size of the dimensions, size of the real stack.
m_sliceLabels - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: slice labels
m_sliceLabels - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: slice labels
m_sliceLabels - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: slice labels
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Vector of installed StatusListener objects.
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Vector of installed StatusListener objects.
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: vector of installed StatusListeners
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: vector of installed StatusListeners
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Vector of installed StatusListener objects.
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage: vector of installed StatusListeners
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: vector of installed StatusListeners
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: vector of installed StatusListeners
m_title - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Image title This member is private to enforce access via the corresponding setter/getter only.
m_type - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: MiToBo image type
m_width - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Width of input image.
mad - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
mad - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Maximal allowed discrepancy.
mahalanobis(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
main(String[]) - Static method in class cmdTools.cellAnalysis.ParticleDetector2D
main(String[]) - Static method in class cmdTools.mtb_imagetools.ImageConvert
main(String[]) - Static method in class cmdTools.tracking.multitarget.EvalTracks
main(String[]) - Static method in class cmdTools.tracking.multitarget.ObservationSeriesGenerator
main(String[]) - Static method in class cmdTools.tracking.multitarget.ObservationsInfo
main(String[]) - Static method in class cmdTools.tracking.multitarget.RBMCDATracker
main(String[]) - Static method in class cmdTools.visualization.DisplayImage
main(String[]) - Static method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs: Test function.
main(String[]) - Static method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN4: Test
main(String[]) - Static method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN8: Test
mainFrame - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

The top level frame.
mainFrame - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Main window frame.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel: Main panel.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel: Main panel.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel: Main panel containing all graphical components.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser: Main panel.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

The top level panel of this frame.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Main panel of main frame.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Main panel of main frame.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Main panel of main frame.
mainpath - Variable in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree: Root directory of the tree.
makeline(int, int, int, int, Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Draws a line between two points.
makePolySimple(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper: Simplifies the given polygon.
makeSimple() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Makes the polygon simple, i.e. removes self-overlaps.
makeSimple() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
makeTable() - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
makeTable() - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
makeTable() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Create the result table and include the specific table header.
makeTable() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer: create results table
makeTable() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
makeTable(MTBRegion2DSet, MTBImage, int, int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: create results table
makeTable() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: create result table
makeTable() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D: create result table
ManualTrackingMigrationAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
ManualTrackingMigrationAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
ManualTrackingMigrationAnalyzer(String) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
ManualTrackingTrajectoryExtraction - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
ManualTrackingTrajectoryExtraction(String, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
map - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Map for value mappings.
mapHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Height of class map.
mapIndexToValue(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
mapMaxX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Maximal x coordinate of class map.
mapMaxY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Maximal y coordinate of class map.
mapMinX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Minimal x coordinate of class map.
mapMinY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Minimal y coordinate of class map.
mapWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Width of class map.
MARGIN - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
marginRoughnessValues - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
markBranchPoints(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Mark branch/special points as first step before building up the whole skeleton graph.
markerVects - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Set of available marker vectors.
markov - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter: Markov matrix probability of dynamic model switching: A matrix with size (#dynamicmodels x #dynamicmodels).
mask - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
mask - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Mask to exclude image regions and tiles, respectively.
mask - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
mask - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Optional mask for excluding image regions from processing.
mask - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D: Mask.
maskCenterX - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
maskCenterY - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
maskChannel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
maskDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Directory with (cell) masks.
maskDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: (Optional) directory with (cell) boundaries.
maskDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Directory with (cell) masks.
maskFormat - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Format of provided cell masks.
maskFormat - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Format of provided cell boundaries.
maskFormat - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Format of provided cell masks.
maskHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker: Height of the mask to be generated.
maskImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
maskImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
maskIO - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to read a binary image.
MaskMaker(MTBSnake, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker: Default constructor with zero offsets.
MaskMaker(MTBSnake, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker: Constructor with non-zero offsets.
maskRadiusC - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
maskRadiusT - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
maskRadiusX - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
maskRadiusY - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
maskRadiusZ - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
maskShape() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.maskShape
maskSize - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
maskSize - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgClose
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgErode
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
maskSizeX - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
maskSizeY - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
maskWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker: Width of the mask to be generated.
matchesRootSegmentStatusToDraw(EnumSet<Drawing.ROOTSEGMENT_STATUS>, MTBXMLRootSegmentStatusType.Enum) - Static method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing
MatchingAdjacencyMatrix - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts: Abstract class of an adjacency matrix for graph matching, i.e. graph nodes are associated to different partitions.
MatchingAdjacencyMatrix() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.MatchingAdjacencyMatrix
MatchingBipartite - Class in de.unihalle.informatik.MiToBo.math.optimization: Base class for bipartite matching algorithms.
MatchingBipartite() - Constructor for class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite: Default constructor.
MatchingBipartite_HungarianAlgorithm - Class in de.unihalle.informatik.MiToBo.math.optimization: Bipartite matching with Hungarian algorithm.
MatchingBipartite_HungarianAlgorithm() - Constructor for class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Default constructor.
MatchingBipartite_HungarianAlgorithm(double[][], MatchingBipartite_HungarianAlgorithm.ScoreInterpretation) - Constructor for class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Default constructor with parameters.
MatchingBipartite_HungarianAlgorithm.ScoreInterpretation - Enum in de.unihalle.informatik.MiToBo.math.optimization: Matrix scores interpretation.
matchingMatrix - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Matching matrix.
matchingMatrix - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Matching matrix.
matchParticles(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Match particle regions to nuclei regions.
MathHelper - Class in de.unihalle.informatik.MiToBo.apps.xylem
MathHelper() - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
MathX - Class in de.unihalle.informatik.MiToBo.math: Math class with functions that are not provided by Java's Math class.
MathX() - Constructor for class de.unihalle.informatik.MiToBo.math.MathX
MathXGeom - Class in de.unihalle.informatik.MiToBo.math: Math class with helper functions for basic geometric operations.
MathXGeom() - Constructor for class de.unihalle.informatik.MiToBo.math.MathXGeom
matrixScore - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Score interpretation.
matrixSize - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Number of rows and columns, respectively.
max - Variable in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
max(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Pixelwise maximum
max(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Pixelwise maximum
MAX_ALLOWED_NUM_PHASES - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Maximal number of phases which may be represented including background phase.
max_d2c - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Maximum peak distance factor.
MAX_VALUE - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Constant used in SDF calculations.
maxAlpha - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Maximal possible value of alpha as can be provided by parameter updated.
maxAngle - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Maximal orientation where to end.
maxArea - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
maxAreaChange - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
maxAreaChange - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
maxAssociatedTargetID() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
maxAssociatedTargetID() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation: Get the maximum target id associated by this data association object
maxAxisLengths - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: List of maximal axis lengths of plastid regions.
maxBeta - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Maximal possible value of beta.
maxBitsSoFar - Static variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs: Maximal bit number for which the class has already been initialized.
maxColor - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper: Color for maximal value.
maxColor - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Color for maximal value.
maxCompDist - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Maximal distance of adjacent components.
maxCompSize - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Minimal size of components in mode ERASE_SMALL_COMPS.
maxCoreRegionWidths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
maxDiffusionDist - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
maxDilMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
maxDist - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
maxDist - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
maxDist - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
maxDist - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: Maximal distance of points within the neighborhood to current pixel, i.e. the pixel which neighborhood we are considering
maxDistNeighbors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
maxDistNeighbors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN: Maximum distance of neighboring observations
maxEnergyVal - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Maxmimum value of energy, dependent on number of snakes and rho.
maxExpansion - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Maximum expansion by Voronoi dilation.
maxFragmentDistance - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
maxFragmentDistance - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Maximum distance to connect a fragment to a detected neuron, given in pixel.
maximalCellSize - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Threshold for the maximal admissible cell size.
maximalCellSize - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Threshold for the maximal admissible cell size.
maxIncreaseFraction - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
maxIndexMap - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Map of indices of maximal responses.
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
maxIter - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
maxIterations - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
maxIterations - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Number of snake iterations.
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff: Maximum number of iterations.
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations: Maximum number of iterations.
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff: Maximum number of iterations.
maxLabel - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Maximal label appearing in the label list.
maxLabel - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: Maximal label appearing in the label list.
maxLevels - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Maximum number of levels to perform.
maxLineLength - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Maximal line length.
maxLineLength - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Maximal line length.
maxNumNeighbors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
maxNumNeighbors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN: Maximum number of neighboring observations
maxradius - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Maximal radius of region to be considered for intensity normalization.
maxRegionCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Maximum number of regions in groundtruth or segmented region set.
maxRegionCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Maximum number of regions in groundtruth or segmented region set.
maxScale - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.ResponseDifference: Upper vessel scale.
maxSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Maximum size of regions.
maxSizeValue - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper: Maximal value threshold.
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor: Maximal allowed length of a branch to be accepted as spine.
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Maximum length to define a branch of a neurite as spine (filopodia-like protrusion) in pixel.
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Given maximum lengths for definition of spines.
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor: Maximal allowed length of a branch to be accepted as spine.
maxTargetID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
maxTargetID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample: The maximum target ID that occurred in this sample up to the current time step
maxVal - Variable in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization: Maximal value of intensity range, depending on input image type.
maxValidNeighborCount - Static variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapterRIU: Maximal neighbor number for which array has been initialized so far.
maxVar - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Maximum instability score, should be in the interval of [0,1].
maxVoronoiExpDist - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Voronoi expansion distance.
maxWeight - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
maxWeights - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
maxWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Expected width of thick vessels.
mBorder - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape: Border of the object.
mCurve - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeCurve: Curve object representing the shape of the marker.
mean - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution: mean vector
mean - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
mean - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Average vector of input dataset.
mean - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
mean - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
meanAndVariance(int[]) - Static method in class cmdTools.tracking.multitarget.ObservationsInfo
meanAreas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
MeanFilter - Class in de.unihalle.informatik.MiToBo.filters.linear: Multidimensional mean filter
MeanFilter() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Constructor with default parameters sizeX=1, sizeY=1, sizeZ=0, sizeT=0, sizeC=0, kernelTruncation=3, sizeInterpretation=PHYSICALSIZE.
MeanFilter(MTBImage, Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Constructor for mean filtering in x- and y-dimension.
MeanFilter(MTBImage, Integer, Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Constructor for mean filtering in x-, y- and z-dimension.
MeanFilter(MTBImage, Integer, Integer, Integer, Integer, Integer, MTBImageWindow.BoundaryPadding) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Constructor for mean filtering.
meanFilter() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: compute the mean filter
meanFilterSize - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Size of mean filter for Gaussian derivative image.
meanfreeData - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Normalized, i.e., mean-free, dataset.
meanfreeDataMatrix - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Normalized, i.e., mean-free, data matrix.
meaningfulNodes(MTBTreeNode, MTBImage[], MTBImageHistogram[], int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Get the most meaningful regions from a (sub)tree.
meanOfRegion(MTBRegion2D, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
means - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Average intensities per region, first index refers to channel.
means - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Average intensities.
meanX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
measure() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter: measures the scratch area, i.e. number of pixels that don't have value 0
Measure_DetectionErrors - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures: This class implements 3 detection errors for contour detection evaluation.
Measure_DetectionErrors() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors: Default constructor.
Measure_DetectionErrors(MTBImageShort, MTBImageShort, ArrayList<ArrayList<Point>>, ArrayList<ArrayList<Point>>, ArrayList<Integer>, ArrayList<Integer>, byte[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors: Constructor with arguments.
Measure_HausdorffDistance - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures: The class implements the Hausdorff Distance for contour detection evaluation.
Measure_HausdorffDistance() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_HausdorffDistance: Default constructor.
Measure_HausdorffDistance(MTBImageShort, MTBImageShort, ArrayList<ArrayList<Point>>, ArrayList<ArrayList<Point>>, ArrayList<Integer>, ArrayList<Integer>, byte[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_HausdorffDistance: Constructor with arguments.
Measure_OdetsCriteria - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures: This class implements Odet's contour detection evaluation criteria for oversegmentation (OCO) and undersegmentation (OCU).
Measure_OdetsCriteria() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria: Default constructor.
Measure_OdetsCriteria(MTBImageShort, MTBImageShort, ArrayList<ArrayList<Point>>, ArrayList<ArrayList<Point>>, ArrayList<Integer>, ArrayList<Integer>, byte[][], int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria: Constructor with arguments.
Measure_PrattsFigureOfMerit - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures: This class implements Pratt's figure of merit for contour detection evaluation.
Measure_PrattsFigureOfMerit() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_PrattsFigureOfMerit: Default constructor.
Measure_PrattsFigureOfMerit(MTBImageShort, MTBImageShort, ArrayList<ArrayList<Point>>, ArrayList<ArrayList<Point>>, ArrayList<Integer>, ArrayList<Integer>, byte[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_PrattsFigureOfMerit: Constructor with arguments.
Measure_RecallPrecisionF - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures: Class for evaluating recalls, precisions, F1-scores and Jaccard indices.
Measure_RecallPrecisionF() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_RecallPrecisionF: Default constructor.
Measure_RecallPrecisionF(MTBImageShort, MTBImageShort, TreeSet<Integer>, TreeSet<Integer>, int[], int[], HashMap<Integer, Integer>, HashMap<Integer, Integer>, int, int, double[][], byte[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_RecallPrecisionF: Default constructor with parameters.
measureInfo - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Info string to structure GUI.
MeasurementUnits() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.MeasurementUnits
MeasureUnit() - Constructor for enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResultEnums.MeasureUnit
measureUnits - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Units to be used for measurements.
measureUnits - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Units for measurements.
MedialnessMultiScaleFilter2D - Class in de.unihalle.informatik.MiToBo.filters.vesselness: 2D multi-scale medialness filter for vessel segmentation.
MedialnessMultiScaleFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Standard constructor.
MedialnessMultiScaleFilter2D(MTBImage, Integer, Double, Double, Double, MedialnessMultiScaleFilter2D.FilterMode, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Constructor to create a new 2D multi-scale medialness filter.
MedialnessMultiScaleFilter2D.FilterMode - Enum in de.unihalle.informatik.MiToBo.filters.vesselness: Settings.
memA - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Optimization matrix with values of last calculations.
memoryMode - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: In memory mode labels can be transferred from one region to another.
method - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
MFFDOGFilter2D - Class in de.unihalle.informatik.MiToBo.filters.vesselness: MF-FDOG filter for vessel segmentation.
MFFDOGFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Default constructor.
MFFDOGFilter2D.VesselMode - Enum in de.unihalle.informatik.MiToBo.filters.vesselness: Detection scenario mode.
MFFDOGMultiScaleFilter2D - Class in de.unihalle.informatik.MiToBo.filters.vesselness: MF-FDOG multi-scale filter for vessel segmentation.
MFFDOGMultiScaleFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D: Default constructor.
Mica2D - Class in de.unihalle.informatik.MiToBo.apps.cells2D: Operator for integrated cell image analysis.
Mica2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Default constructor.
Mica2D(MTBImage, int, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Default constructor.
Mica2DTableModel - Class in de.unihalle.informatik.MiToBo.apps.cells2D: Implementation of a TableModel for the Granule Detector result table.
Mica2DTableModel(int, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel: Default constructor.
midPoint - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Median point of contour.
midPointPosOnContour - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Index of median segment pixel on contour.
MigrationAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D: Operator for analyzing the movement pattern of cells as well as changes in morphology and fluorescence intensity
MigrationAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
MigrationAnalyzer(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
MigrationAnalyzer(MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
min - Variable in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
min(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Pixelwise minimum
min(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Pixelwise minimum
MIN_SE_SIZE - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Minimum size of an SE.
minAngle - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Minimal orientation from where to start.
minArea - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
minArea - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
minAreaAfterErosion - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: The minimum size of regions after the erosion to get preserved.
minAreaAfterOpening - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: Minimal area (in pixels) of a region required after opening.
minAreaAfterOpeningInitSeg - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: Minimal area (in pixels) of a region required after opening.
minAreaGrowth - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Lower threshold for region growth.
minAreaPostProcessing - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: The minimum size of a MTBRegion2D to not be removed (after opening the grown regions).
minAreaPostProcessing - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: The minimum size of a MTBRegion2D to not be removed (after opening the grown regions).
minAreaSeedRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: The minimum size of a MTBRegion2D to further erode when computing seed regions.
minAreaSeedRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: The minimum size of a MTBRegion2D to further erode when computing seed regions.
minAxisLengths - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: List of minimal axis lengths of plastid regions.
minColor - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper: Color for minimal value.
minColor - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Color for minimal value.
minCompactness - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: Minimal compactness of a region required after opening.
minCompactnessInitSeg - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: Minimal compactness of a region required after opening.
minCompSize - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Minimal size of components in mode ERASE_SMALL_COMPS.
minCoreRegionWidths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
minDilMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
minDiversity - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Minimum diversity score, should be in the interval of [0,1].
minimalBorderLength - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Lower threshold for border length.
minimalCellSize - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Threshold for the minimal admissible cell size.
minimalCellSize - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Threshold for the minimal admissible cell size.
minimalCurvature - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Threshold for minimal curvature.
minIndentationLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Minimal number of pixels a valid indentation requires.
minIntensityVariance - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Minimum admissible variance in new snake interior fractions..
minLineLength - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Minimal line length.
minLineLength - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Minimal line length.
minMN - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Minimum of number of observations and number of targets
minNucleusSize - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Minimal size of valid nuclei regions.
minProtrusionLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Minimal number of pixels a valid protrusion requires.
minRegionCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Minimum number of regions in groundtruth or segmented region set.
minRegionCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Minimum number of regions in groundtruth or segmented region set.
minRegionSize - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Minimal size of valid regions.
minRegionSize - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT: Minimal size of valid regions.
minScale - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.ResponseDifference: Lower vessel scale.
minSeedSize - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
minSeedSize - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
minSize - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
minSize - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
minSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Minimum size of regions.
minSizeFraction - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
minSizeValue - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper: Minimal size threshold.
MinSnakePointNum - Static variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Minimum number of points acceptable for snakes.
minStructureSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Minimal size of structure regions to be considered.
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
minW - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Estimated width of linear structures in vesselness enhancement filtering.
minWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Expected width of thin vessels.
mitoboIcon - Variable in class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon: The icon by itself.
MixtureDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl: A distribution represented by a mixture of distributions
MixtureDistribution(ProbabilityDensityFunction[]) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
MixtureDistribution(ProbabilityDensityFunction[], double[]) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution: Constructor
mmID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID: motion-model-ID
mode - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Detection mode.
mode - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Converter mode/algorithm
Mode() - Constructor for enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.Mode
mode - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D: Mode of application.
mode - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Mode for detecting vessels.
mode - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D: Scenario for detecting vessels.
mode - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Scenario for detecting vessels, i.e. relation of foreground to background.
mode - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Mode for dimension reduction, i.e., how to determine the sub-space dimensionality.
mode - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
Mode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack.Mode
model - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
modelFile - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
modelTransition - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
modelTransition - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
modeSelection - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
modeSelection - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
modeSelectLabelImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Button to select label image mode.
modeSelectMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Button to select binary mask mode.
modeSelectRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Button to select region set mode.
modeSelectShape - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Button to select shape mode.
modeSelectThreshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Button to select image thresholding mode.
modificationMode - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
moleculeChannels - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
moleculeChannels - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
moleculeImage - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
molecules - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
morphFeatureOp - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Operator to analyze morphology of cells.
morphGradient(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
morphMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Mask size to be used in morphological pre-/postprocessing.
MorphologyAnalyzer2D - Class in de.unihalle.informatik.MiToBo.features: Operator to extract shape and region features for given regions.
MorphologyAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
MorphologyAnalyzer2D(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: constructor
MorphologyAnalyzer2D(MTBRegion2DSet) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
MorphologyAnalyzer2D.FeatureNames - Enum in de.unihalle.informatik.MiToBo.features: Set of region features calculated from segmented cell regions.
MorphologyAnalyzer2DInProData - Class in de.unihalle.informatik.MiToBo.features: Data type for protrusion/indentation analysis of region contours.
MorphologyAnalyzer2DInProData(MTBContour2D, int) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Default constructor.
MorphologyAnalyzer2DInProData.InflectionPoint - Class in de.unihalle.informatik.MiToBo.features: Class to represent inflection points.
MorphologyAnalyzer2DInProData.InProContourSegment - Class in de.unihalle.informatik.MiToBo.features: Class to represent concave/convex segments along a contour.
MorphologyAnalyzer2DInProData.SegmentType - Enum in de.unihalle.informatik.MiToBo.features: Type of segment to distinguish between indentation and protrusions.
MorphologyAnalyzer2DInProHelper - Class in de.unihalle.informatik.MiToBo.features: Helper functions for analyzing protrusions and indentations along a contour.
MorphologyAnalyzer2DInProHelper(int, int, double, MTBImage, MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper: Default constructor.
MorphologyAnalyzer3D - Class in de.unihalle.informatik.MiToBo.features
MorphologyAnalyzer3D() - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
MorphologyAnalyzer3D(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
MorphologyAnalyzer3D(MTBRegion3DSet, MTBSurface3DSet) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
morphOp - Variable in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
motionFraction - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
motionFraction - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Minimum fraction of points which should have stooped to move until the snake optimization stops.
motionFraction - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff: Motion fraction factor.
MotionModelID - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl: A target-ID class that additionally hold a "motion model"-ID.
MotionModelID(short, byte) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID: Constructor.
MotionModelID(MTBXMLMotionModelIDType) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID: Constructor with the corresponding XML-Type.
mouseClicked(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
mouseClicked(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
mouseDragged(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
mouseEntered(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
mouseEntered(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
mouseExited(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
mouseExited(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
mouseMoved(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
mousePressed(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
mousePressed(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
mouseReleased(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
mouseReleased(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
MPH_EXTENSION - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess: Default extension of MiToBo processing history file.
MPMFFilter2D - Class in de.unihalle.informatik.MiToBo.filters.vesselness: Multiscale Production of the Matched Filter (MPMF) implementation.
MPMFFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Default constructor.
MPMFFilter2D.ResponseDifference - Class in de.unihalle.informatik.MiToBo.filters.vesselness: Function to find roots during middle scale calculation.
MPMFFilter2D.VesselMode - Enum in de.unihalle.informatik.MiToBo.filters.vesselness: Detection scenario mode.
mPolygon - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapePolygon: Region object representing the shape of the marker.
mRegion - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeRegion: Region object representing the shape of the marker.
mserCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Count of detected MSERs.
MTBActiveContourEnergy - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: Common interface for active contour energies.
MTBActiveContourEnergy_CVRegionFit - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.energies: Active contour energy implementing Chan-Vese region fitting for gray-scale and vector-valued, i.e. multi-channel, images.
MTBActiveContourEnergy_CVRegionFit() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Default constructor.
MTBActiveContourEnergy_CVRegionFit(MTBImage, double[], double[]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Default constructor with arguments.
MTBActiveContourEnergy_MeanSep - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.energies: Active contour energy based on region mean separation.
MTBActiveContourEnergy_MeanSep() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Default constructor.
MTBActiveContourEnergy_MeanSep(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Default constructor with parameter.
MTBActiveContourEnergyComputable - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: Common interface for active contour energies used in non-PDE contexts.
MTBActiveContourEnergyDerivable - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: Common interface for active contour energies used in PDE contexts.
MTBActiveContourException - Exception in de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions: MiToBo exception thrown in context of segmentation with active contours.
MTBActiveContourException(MTBActiveContourException.ExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException: Default constructor.
MTBActiveContourException.ExceptionType - Enum in de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions: Possible exception types.
MTBAwtPoint2DDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Data I/O class for Point2D.Double.
MTBAwtPoint2DDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing
MTBAwtPoint2DDataIOSwing.PointConfigPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Panel to display and read 2D points.
MTBBatchInputImageDataIterator(String, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator: Default constructor.
MTBBorder2D - Class in de.unihalle.informatik.MiToBo.core.datatypes: Datatype to represent borders of components.
MTBBorder2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Standard constructor.
MTBBorder2D(Vector<Point2D.Double>, MTBBorder2D.BorderConnectivity) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Constructor to create a 2D border object from a 2D point vector.
MTBBorder2D.BorderConnectivity - Enum in de.unihalle.informatik.MiToBo.core.datatypes: Kind of neighborhood to be applied to border pixels.
MTBBorder2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes: A set of 2D borders.
MTBBorder2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Standard constructor.
MTBBorder2DSet(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Construct an empty set of borders with given extent of domain.
MTBBorder2DSetROI - Class in de.unihalle.informatik.MiToBo.core.imageJ: Class to visualize and handle a MTBBorder2DSet in the ImageJ ROI-Manager.
MTBBorder2DSetROI(Roi) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI: Constructor of super class.
MTBBorder2DSetROI(MTBBorder2DSet, String) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI: Constructor to create a new Roi-Manager-Object, based on a MTBBorder2DSet.
MTBChanVeseEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: A class to implement the Chan-Vese energy for nonPDE level sets.
MTBChanVeseEnergyNonPDE(double, double, double[], double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE: Construct an energy object realizing the Chan-Vese energy.
MTBChanVeseEnergyNonPDE(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE: Construct an energy object realizing the Chan-Vese energy.
MTBChanVeseEnergyNonPDE(MTBImage, MTBLevelsetMembership, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE: Construct an energy object realizing the Chan-Vese energy.
MTBChanVeseEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE: Construct an energy object for the level set function realizing the Chan-Vese energy.
MTBChooseOpNameFrame - Class in de.unihalle.informatik.MiToBo.core.gui: Main window for selecting MiToBo annotated operators for running.
MTBChooseOpNameFrame() - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame: Constructor.
MTBConstants - Class in de.unihalle.informatik.MiToBo.core.datatypes.defines: Constants globally defined for MiToBo.
MTBConstants() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.defines.MTBConstants
MTBContour2D - Class in de.unihalle.informatik.MiToBo.core.datatypes: Class to create 2D contour objects with a vector of points, belonging to the contour.
MTBContour2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Standard constructor.
MTBContour2D(Vector<Point2D.Double>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Constructor to create a 2D contour object from a 2D point vector.
MTBContour2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes: A set of 2D contours living in a common domain which is a rectangular subset of R x R.
MTBContour2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Standard constructor.
MTBContour2DSet(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Construct an empty set of contours with given extent of domain.
MTBContour2DSetROI - Class in de.unihalle.informatik.MiToBo.core.imageJ: Class to visualize and handle a MTBContour2DSet in the ImageJ ROI-Manager.
MTBContour2DSetROI(Roi) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI: Constructor of super class.
MTBContour2DSetROI(MTBContour2DSet, String) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI: Constructor to create a new Roi-Manager-Object, based on a MTBContour2DSet.
MTBCVFittingEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: A class to implement the fitting term of the Chan-Vese energy for level sets using a non PDE approach to optimization.
MTBCVFittingEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE: Construct an energy object for the level set function phi realizing the fitting term of the Chan-Vese energy.
MTBCVFittingEnergyNonPDE(double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE: Construct an energy object realizing the fitting term of the Chan-Vese energy.
MTBCVFittingEnergyNonPDE(double, double, double[]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE: Construct an energy object realizing the fitting term of the Chan-Vese energy.
MTBCVFittingEnergyNonPDE(MTBImage, MTBLevelsetMembership, double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE: Construct an energy object with the initial level set function phi realizing the fitting term of the Chan-Vese energy to segment img.
MTBDataExportableToImageJROI - Interface in de.unihalle.informatik.MiToBo.core.datatypes.interfaces: Interface for MiToBo data types which can be exported to ImageJ ROIs.
MTBDataIOFile - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline: DataIO provider (for commandline-OpRunner) for classes that can only be read from and written to file.
MTBDataIOFile() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile
MTBDataIOFile.MTBDataIOFileButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
MTBDataIOFileButton(Class<?>, Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
MTBDataIOFileInPanel(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel: Default constructor.
MTBDataIOFileOutPanel(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel: Default constructor.
MTBDataIOFileSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Data I/O provider for GUI-OpRunner supporting MiToBo container classes Provides data I/O for the following classes:
MTBRegion2DSetBag
MTBRegion2DSet
MTBRegion3DSet
MTBPolygon2DSet
MTBContour2DSet
MTBBorder2DSet
MTBLineSegment2DSet
Note that some of the classes allow for interaction with the ROI manager of ImageJ, i.e. the class MTBPolygon2DSet.
MTBDataIOFileSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
MTBDataIOFileSwing.InputMode - Enum in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Input mode for data.
MTBDataIOFileSwing.MTBDataIOFileInPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Panel for handling GUI I/O of MiToBo container classes.
MTBDataIOFileSwing.MTBDataIOFileOutPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Panel for displaying and saving MiToBo container classes.
MTBDataIOFileSwing.OutputMode - Enum in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Output mode for data.
MTBDataIOFileXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans: DataIO provider for xmlbeans for classes that can only be read from and written to file.
MTBDataIOFileXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBDataIOFileXmlbeans
MTBDatatypeException - Exception in de.unihalle.informatik.MiToBo.core.exceptions: MiToBo exception type related to problems with data types in general.
MTBDatatypeException(MTBDatatypeException.DatatypeExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException: Default constructor.
MTBDatatypeException.DatatypeExceptionType - Enum in de.unihalle.informatik.MiToBo.core.exceptions: Possible exception types.
MTBDoubleData - Class in de.unihalle.informatik.MiToBo.core.datatypes.wrapper: A double to be used as input or output for MTB operators.
MTBDoubleData(Double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData: Construct an empty double data object from the given double value.
MTBEnergySumNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
MTBEnergySumNonPDE(String, Vector<MTBGenericEnergyNonPDE>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE: Construct an energy object for a level set function realizing the sum of energies in the vector energies.
MTBEnergySumNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE: Construct an energy object for a level set function realizing the sum of energies.
MTBEnvironmentConfig - Class in de.unihalle.informatik.MiToBo.core.helpers: This class extends the super class with routines to access ImageJ properties.
MTBEnvironmentConfig() - Constructor for class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
MTBException - Exception in de.unihalle.informatik.MiToBo.core.exceptions: MiToBo specific exception type.
MTBException() - Constructor for exception de.unihalle.informatik.MiToBo.core.exceptions.MTBException
MTBGammaFixed - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize: Class for gamma adaptation with a fixed decreasing factor for all gamma values.
MTBGammaFixed() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed: Default constructor.
MTBGammaFixed(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed: Constructor with fixed decreasing factor for adaptation.
MTBGammaNone - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize: Class which is not changing the gamma values.
MTBGammaNone() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone: Standard constructor.
MTBGammaPtWiseExtEner - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize: Class for gamma adaptation depending on the external energy values for each snake control point.
MTBGammaPtWiseExtEner() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner: Standardconstructor
MTBGammaUpdate - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize: Class for adaptive step size calculation of the snake step size gamma.
MTBGammaUpdate() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
MTBGenericEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: The base class for energies intended for a nonPDE level set approach.
MTBGenericEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
MTBGraph - Class in de.unihalle.informatik.MiToBo.core.datatypes: Class implements an (un-) directed MTBGraph.
MTBGraph() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Standard constructor.
MTBGraph(boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Constructor to create an empty undirected or directed MTBGraph.
MTBGraph(Vector<MTBGraphNode<?>>, Vector<MTBGraphEdge>, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Constructor to create an undirected or directed MTBGraph with the given nodes and edges.
MTBGraphEdge - Class in de.unihalle.informatik.MiToBo.core.datatypes: Class implements MTBGraphEdges for the MTBGraph.
MTBGraphEdge(MTBGraphNode<?>, MTBGraphNode<?>, Vector<?>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Constructor to create a new MTBGraphEdge.
MTBGraphEdge(MTBGraphNode<?>, MTBGraphNode<?>, Vector<?>, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Constructor to create a new MTBGraphEdge.
MTBGraphNode<T> - Class in de.unihalle.informatik.MiToBo.core.datatypes: Class implements MTBGraphNodes for the MTBGraph.
MTBGraphNode(T) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Constructor to create a new MTBGraphNode object.
MTBGrappaFrame - Class in de.unihalle.informatik.MiToBo.core.grappa: Main frame of Grappa graphical editor for MiToBo.
MTBGrappaFrame(Collection<ALDOperatorLocation>, Collection<ALDOperatorLocation>) - Constructor for class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaFrame: Default constructor
MTBGrappaWorkbench - Class in de.unihalle.informatik.MiToBo.core.grappa: Main frame of Grappa in MiToBo context.
MTBGrappaWorkbench(MTBGrappaFrame) - Constructor for class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench: Default constructor
MTBGrappaWorkbenchTab - Class in de.unihalle.informatik.MiToBo.core.grappa: Grappa workflow graph.
MTBGrappaWorkbenchTab(MTBGrappaWorkbench, ALDGrappaWorkbenchGraph) - Constructor for class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab: Default constructor
MTBGrappaWorkbenchTab(ALDGrappaWorkbench, mxGraph, ALDWorkflow) - Constructor for class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab: Constructor to setup tab from given (reloaded) workflow.
MTBGroundtruthEvaluationData - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation: Data object containing evaluation data from groundtruth comparison.
MTBGroundtruthEvaluationData(HashMap<String, HashMap<Integer, Double>>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.MTBGroundtruthEvaluationData: Default constructor.
MTBHistoryImageBox(MTBImage, ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox: Default constructor for an image pair.
MTBHistoryImageBox(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox: Default constructor for an MTBImage without associated ImagePlus.
MTBHistoryImageBox(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox: Default constructor for an ImagePlus without linked MTBImage.
MTBIcon - Class in de.unihalle.informatik.MiToBo.core.helpers: Singleton class to provide access to MiToBo icon in graphical environments.
MTBIcon() - Constructor for class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon: Default constructor.
MTBImage - Class in de.unihalle.informatik.MiToBo.core.datatypes.images: Abstract wrapper class for easy access to hyperstacks.
MTBImage(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Constructor.
MTBImage() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Constructor for initializing an empty image (dimension sizes = -1).
MTBImage.FactoryMethod - Enum in de.unihalle.informatik.MiToBo.core.datatypes.images: methods to create new image from an existing one. used in MTBImageFactory
MTBImage.MTBImageFactory - Class in de.unihalle.informatik.MiToBo.core.datatypes.images: A class for creating MTBImages which implements the MTBOperator.
MTBImage.MTBImageType - Enum in de.unihalle.informatik.MiToBo.core.datatypes.images: MiToBo image types
MTBImageArithmetics - Class in de.unihalle.informatik.MiToBo.math.images: This class that provides convenience functions for the ImageArithmetics class.
MTBImageArithmetics() - Constructor for class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Constructor.
MTBImageArithmetics(MTBOperator) - Constructor for class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Constructor with calling operator.
MTBImageByte - Class in de.unihalle.informatik.MiToBo.core.datatypes.images: Wrapper class for easy access to Byte (hyper)stacks.
MTBImageByte(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Constructor
MTBImageByte(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Constructor
MTBImageByte(byte[][], int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Constructor
MTBImageConverter - Class in de.unihalle.informatik.MiToBo.core.dataconverter: Convert a MTBImage to any other image and any image type to a MTBImage.
MTBImageConverter() - Constructor for class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
MTBImageDataIO - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline: Implementation of ALDDataIOCmdline interface for MitoBo images.
MTBImageDataIO() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBImageDataIO
MTBImageDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Implementation of ALDDataIOSwing interface for MiToBo images.
MTBImageDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing: Default constructor.
MTBImageDataIOSwing.ImageShowButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Button to display an image on demand.
MTBImageDataIOSwing.ImageShowPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Panel containing the button to display an image on demand.
MTBImageDataIOSwing.JComboBoxImage - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Class for handling images opened in GUI.
MTBImageDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans: Implementation of ALDDataIOCmdline interface for MitoBo images via xmlbeans provider.
MTBImageDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBImageDataIOXmlbeans
MTBImageDouble - Class in de.unihalle.informatik.MiToBo.core.datatypes.images: Class for easy access to Double (hyper)stacks.
MTBImageDouble(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Constructor
MTBImageException - Exception in de.unihalle.informatik.MiToBo.core.exceptions: MiToBo exception type related to problems with its image data types.
MTBImageException(String) - Constructor for exception de.unihalle.informatik.MiToBo.core.exceptions.MTBImageException: Default constructor.
MTBImageFactory() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
MTBImageFactory(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory: Duplicate constructor
MTBImageFactory(MTBImage, MTBImage.MTBImageType, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory: Convert constructor
MTBImageFactory(MTBImage, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory: Get slice constructor
MTBImageFactory(MTBImage, int, int, int, int, int, int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory: Create a new image from the specified image part
MTBImageFloat - Class in de.unihalle.informatik.MiToBo.core.datatypes.images: Wrapper class for easy access to Float (hyper)stacks.
MTBImageFloat(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Constructor
MTBImageFloat(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Constructor
MTBImageHistogram - Class in de.unihalle.informatik.MiToBo.core.datatypes: Class for generating intensity histograms of objects from class MTBImage.
MTBImageHistogram() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: Default constructor.
MTBImageHistogram(MTBImage, int, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: construct a histogram for the given input image
with specification of binning and value range
all MTBImage types except RGB type are supported
MTBImageHistogram(MTBImage, MTBImage, int, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: construct a histogram for the given input image only for the pixels specified by a binary mask
all MTBImage types except RGB type are supported
with specification of binning and value range
MTBImageHistogram(MTBImage, MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: construct a new MTBHistogram object from the given MTBImage
the histogram ranges from the smallest image value to the largest image value
MTBImageHistogram(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: construct a new MTBHistogram object from the given MTBImage
the histogram ranges from the smallest image value to the largest image value
MTBImageHistogram(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: construct a new MTBHistogram object from the given MTBImage
number of bins is 256 and the histogram ranges from the smallest
image value to the largest image value
MTBImageHistogram(double[], int, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: Construct new histogram from array of values.
MTBImageHistogram(double[], double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: construct a MTBImageHistogram from histogram data contained in an array
MTBImageInt - Class in de.unihalle.informatik.MiToBo.core.datatypes.images: Class for easy access to Int (hyper)stacks.
MTBImageInt(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Constructor
MTBImageIteratorImageDataPanel(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel: Default constructor.
MTBImageManipulator - Interface in de.unihalle.informatik.MiToBo.core.datatypes.images
mtbImageRef - Variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox: MTBImage object in container.
MTBImageRGB - Class in de.unihalle.informatik.MiToBo.core.datatypes.images: Class for easy access to RGB (hyper)stacks.
MTBImageRGB(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Constructor
MTBImageRGB(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Constructor
MTBImageSet - Class in de.unihalle.informatik.MiToBo.core.datatypes.images: A set of MTBImages stored in a vector.
MTBImageSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
MTBImageSet(MTBImage[]) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
MTBImageShort - Class in de.unihalle.informatik.MiToBo.core.datatypes.images: Wrapper class for easy access to Short (hyper)stacks.
MTBImageShort(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Constructor
MTBImageShort(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Constructor
MTBImageTileAdapter - Class in de.unihalle.informatik.MiToBo.core.datatypes.images: Adapter class to support tile-wise processing of images.
MTBImageTileAdapter(MTBImage, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Default constructor.
MTBImageTileAdapter(MTBImage, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Default constructor.
MTBImageTileAdapter.TileIterator - Class in de.unihalle.informatik.MiToBo.core.datatypes.images: Iterates from top-left to bottom-right over the tiles of an image.
MTBImageType() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageType
MTBImageWindow - Class in de.unihalle.informatik.MiToBo.core.datatypes.images: Class for windowing a MTBImage.
MTBImageWindow(int, int, int, int, int, MTBImageManipulator, MTBImageWindow.BoundaryPadding) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Create a new window on a given source MTBImageManipulator (i.e.
MTBImageWindow.BoundaryPadding - Enum in de.unihalle.informatik.MiToBo.core.datatypes.images: Padding of image: Method of how to obtain pixel values outside the image domain
mtbImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat: MTB input image to work on.
MTBIntegerData - Class in de.unihalle.informatik.MiToBo.core.datatypes.wrapper: an Integer wrapper class to be used as input or output for MTB operators
MTBIntegerData(Integer) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
MTBIteratorImageData - Class in de.unihalle.informatik.MiToBo.core.batch.provider.input.swing: Implementation of ALDBatchInputIteratorSwing for MitoBo images.
MTBIteratorImageData() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
MTBIteratorImageData.MTBBatchInputImageDataIterator - Class in de.unihalle.informatik.MiToBo.core.batch.provider.input.swing: Polygon set iterator class.
MTBIteratorImageData.MTBImageIteratorImageDataPanel - Class in de.unihalle.informatik.MiToBo.core.batch.provider.input.swing: GUI element class for image batch iterator.
MTBJFreeChartDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Implementation of ALDDataIOSwing interface for JFreeChart objects.
MTBJFreeChartDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing: Default constructor.
MTBJFreeChartDataIOSwing.ChartShowButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Button to display a chart on demand.
MTBJFreeChartDataIOSwing.ChartShowPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Panel containing the button to display an image on demand.
MTBLengthEnergyFW2D2PNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Implements the (standard) length energy using forward differences for 2D images and a two phase level set function.
MTBLengthEnergyFW2D2PNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2D2PNonPDE: Constructor
MTBLengthEnergyFW2D2PNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2D2PNonPDE: Constructor
MTBLengthEnergyFW2DMPNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Implements the (standard) length energy using forward differences for 2D images and a multi phase leve lset function.
MTBLengthEnergyFW2DMPNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DMPNonPDE: constructor
MTBLengthEnergyFW2DMPNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DMPNonPDE: constructor
MTBLengthEnergyFW2DNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Implements the (standard) length energy using forward differences for 2D images.
MTBLengthEnergyFW2DNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE: constructor
MTBLengthEnergyFW2DNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE: constructor
MTBLengthEnergyFW3D2PNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Implements the (standard) length energy using forward differences for 3D images and a two phase levelset function.
MTBLengthEnergyFW3D2PNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE: constructor
MTBLengthEnergyFW3D2PNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE: constructor
MTBLengthEnergyFW3DMPNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Implements the (standard) length energy using forward differences for 3D images and a multi phase level set function.
MTBLengthEnergyFW3DMPNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DMPNonPDE: constructor
MTBLengthEnergyFW3DMPNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DMPNonPDE: constructor
MTBLengthEnergyFW3DNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Implements the (standard) length energy using forward differences for 3D images.
MTBLengthEnergyFW3DNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE: constructor
MTBLengthEnergyFW3DNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE: constructor
MTBLengthEnergyFWNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Base class of length energies using forward differences.
MTBLengthEnergyFWNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE: constructor
MTBLengthEnergyFWNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE: constructor
MTBLengthEnergyKB2D2P4NNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Implements the (standard) length energy using length approximation due to Kolmogorov/Boykov for tw0 phases and 4 neighborhood.
MTBLengthEnergyKB2D2P4NNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2P4NNonPDE: constructor
MTBLengthEnergyKB2D2P4NNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2P4NNonPDE: constructor
MTBLengthEnergyKB2D2PNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Implements the (standard) length energy using length approximation due to Kolmogorov/Boykov for two phases.
MTBLengthEnergyKB2D2PNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE: constructor
MTBLengthEnergyKB2D2PNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE: constructor
MTBLengthEnergyKBNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: Base class of length energies using forward differences.
MTBLengthEnergyKBNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE: constructor
MTBLengthEnergyKBNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE: constructor
MTBLengthEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: An class for energies for a nonPDF level set approach based on different length energies of the phases boundaries.
MTBLengthEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE: Constructor
MTBLengthEnergyNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE: Constructor
MTBLevelEnergyDerivable_Area - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable: Level set energy minimizing area enclosed by the zero level.
MTBLevelEnergyDerivable_Area() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area: Default constructor.
MTBLevelEnergyDerivable_CVRegionFit - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable: Implementation of Chan-Vese energy for level set functions.
MTBLevelEnergyDerivable_CVRegionFit() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit: Default constructor.
MTBLevelEnergyDerivable_CVRegionFit(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit: Constructor with given image.
MTBLevelEnergyDerivable_Length - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable: Energy minimizing the length of a level set's isocontour.
MTBLevelEnergyDerivable_Length() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length: Default constructor.
MTBLevelsetEnergyDerivable - Interface in de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable: Interface specifying level set energies to be used with techniques of the calculus of variations.
MTBLevelsetException - Exception in de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions: MiToBo exception thrown inside snake segmentation framework.
MTBLevelsetException(MTBActiveContourException.ExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBLevelsetException: Default constructor.
MTBLevelsetFunctionDerivable - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core: Level set function supporting optimization based on variational calculus.
MTBLevelsetFunctionDerivable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
MTBLevelsetFunctionPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes: Class representing a 3-dimensional level set function.
MTBLevelsetFunctionPDE(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Create a new levelset function.
MTBLevelsetFunctionPDE(int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Constructor to init empty function with safety border.
MTBLevelsetFunctionPDE(int, int, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: create a new levelsetfunction, setting a default handle for derivations on borders
MTBLevelsetFunctionPDE(boolean, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: create a new levelsetfunction, setting a default handle for derivations on borders
MTBLevelsetFunctionPDE(boolean, int, int, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: create a new levelsetfunction, setting a default handle for derivations on borders
MTBLevelsetFunctionPDE(int, int, int, MTBSegmentationInterface, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Constructor to build a level set function from a segmentation object.
MTBLevelsetFunctionPDE(int, int, int, MTBSegmentationInterface, boolean, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Constructor to build a level set function from a segmentation object.
MTBLevelsetFunctionPDE.SortedList<EType> - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes: A genric class representing a sorted list
MTBLevelsetFunctionPDE.SortedListElement<EType> - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes: internal representation of elements
MTBLevelsetMembership - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: A class to hold a level set function where only the membership to a phase is required and represented.
MTBLevelsetMembership(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Constructs a two phase level set function which is initialized with a circle or sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.
MTBLevelsetMembership(int, int, int, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Constructs a two phase level set function which is initialiazed with a circle or sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.
MTBLevelsetMembership(int, int, int, MTBImage, int, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Creates a two phase level set function from an image via thresholding.
MTBLevelsetMembership(MTBLevelsetMembership) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Creates a copy of phi.
MTBLevelsetMembership(int, int, Vector<MTBRegion2D>, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Constructor for given size which is initialized from a list of 2D regions for a 2D level set function.
MTBLevelsetMembership(int, int, MTBRegion2DSet, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Constructor for given size which is initialized from a MTBRegion2DSet for a 2D level set function.
MTBLevelsetMembership(MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Constructor for a two phase level set function from a label image.
MTBLevelsetMembership(MTBImage, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Constructor for a level set function from a label image.
MTBLineSegment2D - Class in de.unihalle.informatik.MiToBo.core.datatypes: Enhanced 2D line segments.
MTBLineSegment2D(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D: Constructor.
MTBLineSegment2D(MTBLineSegment2D) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D: Copy constructor.
MTBLineSegment2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes: A set of 2D line segments.
MTBLineSegment2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: Standard constructor.
MTBMeijeringFittingEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: class that implements the energy functional introduced in O.
MTBMeijeringFittingEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE: constructor
MTBMeijeringFittingEnergyNonPDE(MTBImage, MTBLevelsetMembership) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE: constructor
MTBNeurite2D - Class in de.unihalle.informatik.MiToBo.core.datatypes.neurites: Class for neurite objects.
MTBNeurite2D(MTBNeuriteSkelGraph, Vector<Vector<Point2D.Double>>, Vector<Vector<Line2D.Double>>, MTBRegion2D, int, int[], Vector<Vector<Double>>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Constructor to generate a new neurite object.
MTBNeurite2DProfile - Class in de.unihalle.informatik.MiToBo.core.datatypes.neurites: Container class for storing neurite profile data and associated additional information for a single neurite region.
MTBNeurite2DProfile() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
MTBNeurite2DProfile(MTBNeurite2D, double[], Vector<Vector<Point2D.Double>>, MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile: Constructor to create a new MTBNeuriteProfile object from the given MTBRegion2D.
MTBNeurite2DProfileSet - Class in de.unihalle.informatik.MiToBo.core.datatypes.neurites: A set of neurite profiles organized as linked list.
MTBNeurite2DProfileSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Constructor to create a new set of neurite profiles.
MTBNeurite2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes.neurites: Class to represent a set of MTBNeurite2D objects.
MTBNeurite2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet: Constructor to create a new set of neurites.
MTBNeuriteSkelGraph - Class in de.unihalle.informatik.MiToBo.core.datatypes: The class implements a neurite skeleton graph (NSG), based on the skeleton of a neurite region.
MTBNeuriteSkelGraph() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Standard constructor.
MTBNeuriteSkelGraph(int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Constructor that creates an empty directed MTBNeuriteSkelGraph with defined maximum spine length.
MTBNeuriteSkelGraph(Vector<MTBNeuriteSkelGraphNode<Point2D.Double>>, Vector<MTBGraphEdge>, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Constructor to create an directed MTBNeuriteSkelGraph with the given MTBSkeletonGraphNodes and MTBGraphEdges.
MTBNeuriteSkelGraphException - Exception in de.unihalle.informatik.MiToBo.core.datatypes: Exception handling for MTBSkeletonGraph.
MTBNeuriteSkelGraphException() - Constructor for exception de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphException
MTBNeuriteSkelGraphException(String) - Constructor for exception de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphException
MTBNeuriteSkelGraphNode<T> - Class in de.unihalle.informatik.MiToBo.core.datatypes: Class implements a MTBSkeletonGraphNode, which is a type of the MTBGraphNode.
MTBNeuriteSkelGraphNode(T, MTBNeuriteSkelGraphNode.MTBSkeletonNodeType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode: Constructor to create a new MTBGraphNode object.
MTBNeuriteSkelGraphNode.MTBSkeletonNodeType - Enum in de.unihalle.informatik.MiToBo.core.datatypes: Type of the MTBGraphNode
MTBOperator - Class in de.unihalle.informatik.MiToBo.core.operator: Abstract super class for all MiToBo operators.
MTBOperator() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBOperator: Default constructor.
MTBOperatorCollection<T extends de.unihalle.informatik.Alida.operator.ALDOperatorCollectionElement> - Class in de.unihalle.informatik.MiToBo.core.operator: Class to manage a set of operators.
MTBOperatorCollection(Class<T>) - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorCollection: Default constructor.
MTBOperatorConfigTools - Class in de.unihalle.informatik.MiToBo.core.operator: Helper class for global `MiToBo` operator configuration.
MTBOperatorConfigTools() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools: Hidden constructor, never used outside of the class.
MTBOperatorConfigurationFrame - Class in de.unihalle.informatik.MiToBo.core.gui: Frame to configure an operator's parameters.
MTBOperatorConfigurationFrame(ALDOperator, ALDOpParameterUpdateEventListener) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame: Constructs a control frame for an operator object.
MTBOperatorControlFrame - Class in de.unihalle.informatik.MiToBo.core.gui: This frame is used to display and modify the input parameters of an ALDOperator.
MTBOperatorControlFrame(ALDOperator, ALDOperatorGUIExecutionProxy, ALDOpParameterUpdateEventListener) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame: Construct a JFrame to intantiate and configure an operator opName and use executeOperator to execute this operator if requested by the user.
MTBOperatorControllable - Class in de.unihalle.informatik.MiToBo.core.operator: Operator class with inherent event handling for execution control.
MTBOperatorControllable() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorControllable: Default constructor.
MTBOperatorDocumentationFrame - Class in de.unihalle.informatik.MiToBo.core.gui: Frame to show documentation for operators and tools.
MTBOperatorDocumentationFrame(String, String, String) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorDocumentationFrame: Constructor with title parameter.
MTBOperatorGUIExecutionProxy - Class in de.unihalle.informatik.MiToBo.core.gui: Manager for executing single MiToBo operator and workflow objects via GUI.
MTBOperatorGUIExecutionProxy(ALDOperatorLocation) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorGUIExecutionProxy: Default constructor.
MTBOperatorParameterPanel - Class in de.unihalle.informatik.MiToBo.core.gui: Implementation of panels for MiToBo operator parameters.
MTBOperatorParameterPanel(ALDOperator, Parameter.ExpertMode, boolean, ALDSwingValueChangeListener) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorParameterPanel: Default constructor.
MTBPlotHistogram - Class in de.unihalle.informatik.MiToBo.visualization.drawing: A class to visualize 2D polygons.
MTBPlotHistogram() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram: Default constructor.
MTBPlotHistogram.Histogram - Class in de.unihalle.informatik.MiToBo.visualization.drawing
MTBPlotHistogram.HistogramFrame - Class in de.unihalle.informatik.MiToBo.visualization.drawing
MTBPoint2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
MTBPoint2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet: Standard constructor.
MTBPoint2DSet(List<Point2D>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet: Constructs a MTBPoint2DSet from a list of points.
MTBPoint3D - Class in de.unihalle.informatik.MiToBo.core.datatypes: The Point3D class defines a point representing a location in (x, y, z) coordinate space.
MTBPoint3D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Standardconstructor to create an new empty 3D point object.
MTBPoint3D(double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Construct a new 3D point with the given coordinates.
MTBPoint3D(MTBPoint3D) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Construct a new 3D point from the given 3D point.
MTBPoint3D(MTBXMLPoint3DType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Construct a new MTBPoint3D from a 3D-point object constructed from xml-representation.
MTBPolygon2D - Class in de.unihalle.informatik.MiToBo.core.datatypes: Polygon datatype with double precision.
MTBPolygon2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Default constructor.
MTBPolygon2D(double[], double[], boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Construct polygon from coordinate arrays.
MTBPolygon2D(Vector<Point2D.Double>, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Construct from point list.
MTBPolygon2D.IntersectionPoint2D - Class in de.unihalle.informatik.MiToBo.core.datatypes: Helper class for function simplify().
MTBPolygon2D_GeoPolygonsWrapper - Class in de.unihalle.informatik.MiToBo.core.datatypes: Wrapper class for C2DPolygon functions from GeoPolygons library.
MTBPolygon2D_GeoPolygonsWrapper() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
MTBPolygon2DException - Exception in de.unihalle.informatik.MiToBo.core.datatypes: Exception handling for Polygon2D object.
MTBPolygon2DException() - Constructor for exception de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DException: Standardconstructor.
MTBPolygon2DException(String) - Constructor for exception de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DException: Constructor for new MTBPolygon2DException with specific message output.
MTBPolygon2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes: Data type to represent a set of MTBPolygon2D.
MTBPolygon2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Standard constructor
MTBPolygon2DSet(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Construct an empty set of polygons with given extent of domain.
MTBPolygon2DSet(Vector<MTBPolygon2D>, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Construct polygon set from given vector.
MTBPolygon2DSetROI - Class in de.unihalle.informatik.MiToBo.core.imageJ: Class to visualize and handle a MTBPolygon2DSet in the ImageJ ROI-Manager.
MTBPolygon2DSetROI(Roi) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI: Constructor of super class.
MTBPolygon2DSetROI(MTBPolygon2DSet, String) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI: Constructor to create a new Roi-Manager-Object, based on a MTBPolygon2DSet.
MTBPortHashAccess - Class in de.unihalle.informatik.MiToBo.core.operator: Interface to the port database of the Alida / MiToBo operator history.
MTBPortHashAccess() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess: Constructor without function.
MTBPortHashAccess.MTBHistoryImageBox - Class in de.unihalle.informatik.MiToBo.core.operator: Database object boxing ImagePlus and MTBImage.
MTBQuadraticCurve2D - Class in de.unihalle.informatik.MiToBo.core.datatypes: General quadratic curve.
MTBQuadraticCurve2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Default constructor.
MTBQuadraticCurve2D(double[], boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Constructor.
MTBQuadraticCurve2D.CurveType - Enum in de.unihalle.informatik.MiToBo.core.datatypes: Possible types of curve.
MTBQuadraticCurve2D.DistanceTargetFunction - Class in de.unihalle.informatik.MiToBo.core.datatypes: Distance function for a point's distance to an ellipse.
MTBRegion2D - Class in de.unihalle.informatik.MiToBo.core.datatypes: Class to implement a 2D region object. the region is stored in a vector of 2D double points with its x- and y-coordinate.
MTBRegion2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Construct a new empty MTBRegion2D object.
MTBRegion2D(Vector<Point2D.Double>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Construct a new MTBRegion2D from the given points.
MTBRegion2D(MTBXMLRegion2DType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Construct a new MTBRegion2D from a region object that was constructed from a xml-representation.
MTBRegion2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes: A set of 2D regions living in a common domain which is a rectangular subset of R x R.
MTBRegion2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Standard constructor.
MTBRegion2DSet(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Construct an empty set of regions with given extent of domain
MTBRegion2DSet(Vector<MTBRegion2D>, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Construct an empty set of regions with given extent of domain
MTBRegion2DSet(String) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Construct a set of regions from a xml-file that was written by the write method of this class.
MTBRegion2DSet(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Construct a set of regions from a label image.
MTBRegion2DSet(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Construct a set of regions from a label image.
MTBRegion2DSet(MTBXMLRegion2DSetType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Construct a new MTBRegion2DSet from a region set object that was constructed from a xml-representation.
MTBRegion2DSet.RegionSelector - Class in de.unihalle.informatik.MiToBo.core.datatypes
MTBRegion2DSetBag - Class in de.unihalle.informatik.MiToBo.core.datatypes: A datatype to store multiple MTBRegion2D sets
MTBRegion2DSetBag() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag: Constructor to create an empty bag of region sets
MTBRegion2DSetBag(int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag: Constructor to create an empty bag of region sets with the given capacity
MTBRegion2DSetBag(String) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag: Construct a bag of region sets from a xml-file that was written by the write method of this class.
MTBRegion2DSetBag(MTBXMLRegion2DSetBagType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag: Construct a bag of region sets from a xml-object created by the toXMLType method of this class.
MTBRegion2DSetROI - Class in de.unihalle.informatik.MiToBo.core.imageJ: Class to visualize and handle a MTBRegion2DSet in the ImageJ ROI-Manager.
MTBRegion2DSetROI(Roi) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI: Constructor of super class.
MTBRegion2DSetROI(MTBRegion2DSet, String) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI: Constructor to create a new Roi-Manager-Object, based on a MTBRegion2DSet.
MTBRegion3D - Class in de.unihalle.informatik.MiToBo.core.datatypes: Class to create a 3D region object.
MTBRegion3D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Construct a new MTBRegion3D object.
MTBRegion3D(Vector<MTBPoint3D>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Construct a new MTBRegion3D object from the given points.
MTBRegion3D(Vector<MTBPoint3D>, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Construct a new MTBRegion3D object from the given points and set its id
MTBRegion3D(MTBXMLRegion3DType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Construct a new MTBRegion3D from a 3D-region in xml-representation.
MTBRegion3DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes: A set of 3D regions living in a common domain which is a rectangular subset of R x R.
MTBRegion3DSet(double, double, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Construct an empty set of regions with given extent of domain
MTBRegion3DSet(int, double, double, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Construct an empty set (with memory allocated for N elements) of regions with given extent of domain
MTBRegion3DSet(Vector<MTBRegion3D>, double, double, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Construct an empty set of regions with given extent of domain
MTBRegion3DSet(MTBXMLRegion3DSetType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Construct set of 3D-regions from an xml-representation
MTBRegion3DSet(String) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Construct a set of 3D-regions from a xml-file that was written by the write method of this class.
MTBRegionInterface - Interface in de.unihalle.informatik.MiToBo.core.datatypes: Interface for regions in MiToBo to enable unified handling.
MTBRegionSetInterface - Interface in de.unihalle.informatik.MiToBo.core.datatypes: Interface for region sets in MiToBo to enable unified handling.
MTBRootTree - Class in de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes: Tree datatype to represent plant roots.
MTBRootTree() - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTree: Default constructor.
MTBRootTree(MTBRootTreeNodeData) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTree: Constructor with given data.
MTBRootTree(MTBTreeNode) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTree: Constructor with given root node.
MTBRootTree(MTBPoint2DSet) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTree: Constructor with given set of 2D points.
MTBRootTreeNodeData - Class in de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes: Node data object for MTBRootTree.
MTBRootTreeNodeData() - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Default constructor, all members are initialized with zero.
MTBRootTreeNodeData(double, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Constructor with positional data.
MTBSegmentation2D - Class in de.unihalle.informatik.MiToBo.segmentation.basics: Class for representing 2D segmentations of image data.
MTBSegmentation2D() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Default constructor with empty segmentation.
MTBSegmentation2D(int, int, int, int[][], boolean[][], double[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Constructor.
MTBSegmentation2D(int, int, int, byte[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Constructor.
MTBSegmentation3D - Class in de.unihalle.informatik.MiToBo.segmentation.basics: Class for representing 3D segmentations of image data.
MTBSegmentation3D(int, int, int, int, int[][][], boolean[][][], double[][][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: Constructor.
MTBSegmentationInterface - Interface in de.unihalle.informatik.MiToBo.segmentation.basics: Interface for representing 2D and 3D segmentations of image data.
MTBSegmentationInterface.SegmentationDimension - Enum in de.unihalle.informatik.MiToBo.segmentation.basics: Segmentation dimension datatype.
MTBSet_ActiveContourEnergy - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: Common interface for sets of active contour energies.
MTBSet_ActiveContourEnergyConfigButton(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton: Constructor.
MTBSet_ActiveContourEnergyConfigWindow(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Default constructor.
MTBSet_ActiveContourEnergyDataIOCmdline - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: Class for loading/saving sets of PDE energies for command line interfaces.
MTBSet_ActiveContourEnergyDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline: Default constructor
MTBSet_ActiveContourEnergyDataIOSwing - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: Class for loading/saving sets of PDE energies in GUI contexts.
MTBSet_ActiveContourEnergyDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: GUI element for configuring collections.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: Collection configuration window.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: Internal PDE snake energy GUI table model.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayButton - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: GUI element for showing energy collections.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: Energy collection display window.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow.MTBSet_SnkEnergyPDEGUITableModel - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: Internal GUI table model.
MTBSet_ActiveContourEnergyDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: Class for loading/saving sets of PDE energies for command line interfaces.
MTBSet_ActiveContourEnergyDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOXmlbeans
MTBSet_ActiveContourEnergyDisplayButton(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayButton: Constructor.
MTBSet_ActiveContourEnergyDisplayWindow(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Default constructor.
MTBSet_LevelEnergyDerivable - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core: Container data type for derivable level set energies.
MTBSet_LevelEnergyDerivable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Default contructor for empty set.
MTBSet_LevelEnergyDerivable(Vector<MTBLevelsetEnergyDerivable>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Constructor for a given vector of energies.
MTBSet_LevelEnergyDerivable(Vector<MTBLevelsetEnergyDerivable>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Constructor with energies and weights.
MTBSet_SnakeEnergyComputable - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes: Container data type for snake energies in nonPDE approaches.
MTBSet_SnakeEnergyComputable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable: Default contructor for empty set.
MTBSet_SnakeEnergyComputable(Vector<MTBSnakeEnergyComputable>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable: Constructor for a given vector of energies.
MTBSet_SnakeEnergyComputable(Vector<MTBSnakeEnergyComputable>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable: Constructor with energies and weights.
MTBSet_SnakeEnergyDerivable - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes: Container data type for snake energies in PDE approaches.
MTBSet_SnakeEnergyDerivable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable: Default contructor for empty set.
MTBSet_SnakeEnergyDerivable(Vector<MTBSnakeEnergyDerivable>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable: Constructor for a given vector of energies.
MTBSet_SnakeEnergyDerivable(Vector<MTBSnakeEnergyDerivable>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable: Constructor with energies and weights.
MTBSet_SnkEnergyPDEGUITableModel(int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel: Default constructor.
MTBSet_SnkEnergyPDEGUITableModel(int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow.MTBSet_SnkEnergyPDEGUITableModel: Default constructor.
MTBSetWeightedEnergy<T> - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes: Container data type for energies in PDE approaches.
MTBSetWeightedEnergy() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: Default contructor for empty set.
MTBSetWeightedEnergy(Vector<T>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: Constructor for a given vector of energies.
MTBSetWeightedEnergy(Vector<T>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: Constructor with energies and weights.
MTBSizeEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE: A class to implement the size energy of the Chan-Vese energy.
MTBSizeEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE: Constructor for size energy with weight nu.
MTBSizeEnergyNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE: Constructor for size energy with weight nu.
MTBSkeletonNodeType() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode.MTBSkeletonNodeType
MTBSnake - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes: Active Contour (Snake) datatype.
MTBSnake() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Standard constructor to create a new and empty snake object.
MTBSnake(Vector<MTBSnakePoint2D>, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Constructor to create a new Snake object.
MTBSnake(Vector<MTBSnakePoint2D>, boolean, double, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Constructor to create a new Snake object.
MTBSnake.SnakeCloner - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes: Operator class to construct new snake object from a given one.
MTBSnakeEnergyCD_CVRegionFit - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies: Snake energy based on Chan-Vese region fitting.
MTBSnakeEnergyCD_CVRegionFit() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Default constructor.
MTBSnakeEnergyCD_CVRegionFit(MTBImage, double[], double[]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Default constructor.
MTBSnakeEnergyCD_KassCurvature - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies: Curvature energy of the pioneering paper of Kass et al.
MTBSnakeEnergyCD_KassCurvature() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Default constructor.
MTBSnakeEnergyCD_KassCurvature(double, MTBSnakeEnergyCD_KassCurvature_ParamAdapt) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Constructor with dynamic parameter updater.
MTBSnakeEnergyCD_KassCurvature_ParamAdapt - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt: Parameter adaptation for Kass et al. curvature penalty.
MTBSnakeEnergyCD_KassCurvature_ParamAdapt() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt: Fixed value parameter adaptation for Kass et al. curvature energy.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix: Default constructor.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix(double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix: Construct a new updater for the internal energy using a fixed value.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt: Dummy parameter adaptation for Kass et al. curvature energy.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone: Default constructor.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone: Construct a new updater.
MTBSnakeEnergyCD_KassLength - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies: Internal length penalty energy of the pioneering paper of Kass et al.
MTBSnakeEnergyCD_KassLength() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Default constructor.
MTBSnakeEnergyCD_KassLength(double, MTBSnakeEnergyCD_KassLength_ParamAdapt) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Constructor with dynamic parameter updater.
MTBSnakeEnergyCD_KassLength_ParamAdapt - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt: Parameter adaptation for Kass et al. length penalty.
MTBSnakeEnergyCD_KassLength_ParamAdapt() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
MTBSnakeEnergyCD_KassLength_ParamAdaptFix - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt: Parameter adaptation for Kass et al. length penalty energy by fixed value.
MTBSnakeEnergyCD_KassLength_ParamAdaptFix() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix: Default constructor.
MTBSnakeEnergyCD_KassLength_ParamAdaptFix(double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix: Construct a new updater for the internal energy using a fixed value.
MTBSnakeEnergyCD_KassLength_ParamAdaptNone - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt: Dummy parameter adaptation for Kass et al. length penalty energy.
MTBSnakeEnergyCD_KassLength_ParamAdaptNone() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone: Default constructor.
MTBSnakeEnergyCD_KassLength_ParamAdaptNone(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone: Construct a new updater.
MTBSnakeEnergyCD_OverlapPenalty - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies: Energy to avoid overlaps of snakes in joint optimization of multiple snakes.
MTBSnakeEnergyCD_OverlapPenalty() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Default constructor.
MTBSnakeEnergyCD_OverlapPenalty(double, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Default constructor.
MTBSnakeEnergyCDIB_Distance - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies: Class for external energy from a distance transform (distance map / field).
MTBSnakeEnergyCDIB_Distance() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
MTBSnakeEnergyCDIB_Distance(MTBImageByte, DistanceTransform.DistanceMetric, DistanceTransform.ForegroundColor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance: Constructor to create a new SnakeExternalEnergyDistance object.
MTBSnakeEnergyCDIB_Gradient - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies: External snake energy based on local intensity gradients.
MTBSnakeEnergyCDIB_Gradient() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient: Constructor to create a new SnakeExternalEnergyGradient object.
MTBSnakeEnergyCDIB_Gradient(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient: Constructor to create a new SnakeExternalEnergyGradient object.
MTBSnakeEnergyCDIB_GVF2D - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies: Class for external energy of a GVF field energy vector.
MTBSnakeEnergyCDIB_GVF2D() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D: Default constructor.
MTBSnakeEnergyCDIB_GVF2D(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D: Constructor to create a new SnakeExternalEnergyGVF2D object.
MTBSnakeEnergyCDIB_Intensity - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies: External snake energy based on image intensities.
MTBSnakeEnergyCDIB_Intensity() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity: Default constructor.
MTBSnakeEnergyCDIB_Intensity(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity: Constructor to create a new SnakeExternalEnergyIntensity object.
MTBSnakeEnergyCDImageBased - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies: Interface class for snake energies that are purely image-based.
MTBSnakeEnergyCDImageBased() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
MTBSnakeEnergyComputable - Interface in de.unihalle.informatik.MiToBo.segmentation.snakes.energies: Super class for all energies to be used with greedy snakes in MiToBo.
MTBSnakeEnergyCoupled - Interface in de.unihalle.informatik.MiToBo.segmentation.snakes.energies: Super class for energies working simultaneously on multiple snakes.
MTBSnakeEnergyDerivable - Interface in de.unihalle.informatik.MiToBo.segmentation.snakes.energies: Super class for all energies to be used with PDE snakes in MiToBo.
MTBSnakeException - Exception in de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions: MiToBo exception thrown inside snake segmentation framework.
MTBSnakeException(MTBActiveContourException.ExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBSnakeException: Default constructor.
MTBSnakePoint2D - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes: Class to implement 2D snake points with a special structure: (snake points means control points of the snake, on which the snake energy is calculated and optimized) - every snake point has an old index (position) within the snake, if the point does not exists before, the old index is set to -1 by default - every snake point has a Point2D.Double object for point coordinates
MTBSnakePoint2D() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D: Standard constructor to create a new SnakePoint2D
MTBSnakePoint2D(double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D: Constructor to create a new SnakePoint2D with x- and y-coordinates for the point.
MTBSnakePoint2D(Point2D.Double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D: Constructor to create a new SnakePoint2D from the specified Point2D.Double object.
MTBStringData - Class in de.unihalle.informatik.MiToBo.core.datatypes.wrapper: Class to implement string objects to be used as input or output to MTB operators.
MTBStringData(String) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBStringData: Construct a new MTBStringData object from the given string.
MTBStructuringElement - Class in de.unihalle.informatik.MiToBo.core.datatypes: class representing a 2D flat (, i.e. without different gray values) structuring element
for the use with morphological operations
values are stored in a rectangular 2D array (rows: 1st dimension, columns: 2nd dimension)
whereas onValue represents set locations and 0 represents unset locations
MTBStructuringElement(int[][], int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement: creates structuring element from given 2D-array
MTBStructuringElement(int[][]) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement: creates structuring element from given 2D-array, center is assumed to be at the center of the array
MTBStructuringElement() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement: create quadratic 3x3 structuring element
MTBSummarizerImageData - Class in de.unihalle.informatik.MiToBo.core.batch.provider.output.swing: Implementation of ALDBatchInputIteratorSwing for MitoBo images.
MTBSummarizerImageData() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerImageData
MTBSummarizerRegion2DSet - Class in de.unihalle.informatik.MiToBo.core.batch.provider.output.swing: Implementation of ALDBatchInputIteratorSwing for MitoBo images.
MTBSummarizerRegion2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerRegion2DSet
MTBSummarizerSegResultParticlesMultiChannel - Class in de.unihalle.informatik.MiToBo.core.batch.provider.output.swing: Implementation of ALDBatchInputIteratorSwing for MitoBo images.
MTBSummarizerSegResultParticlesMultiChannel() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerSegResultParticlesMultiChannel
MTBSummarizerTableModel - Class in de.unihalle.informatik.MiToBo.core.batch.provider.output.swing: Implementation of ALDBatchInputIteratorSwing for MTBTableModel.
MTBSummarizerTableModel() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerTableModel
MTBSurface3D - Class in de.unihalle.informatik.MiToBo.core.datatypes: class representing the surface area of a 3D-object
points are not ordered!
MTBSurface3D(Vector<MTBPoint3D>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
MTBSurface3D(Vector<MTBPoint3D>, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
MTBSurface3DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
MTBSurface3DSet(double, double, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Construct an empty set of regions with given extent of domain
MTBTableModel - Class in de.unihalle.informatik.MiToBo.gui: Table model for MiToBo data tables.
MTBTableModel(int, int) - Constructor for class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Default constructor.
MTBTableModel(int, int, Vector<String>) - Constructor for class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Constructor with given header strings.
MTBTableModelDataIO - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline: Class for loading/saving MTBTableModel data objects via commandline.
MTBTableModelDataIO() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
MTBTableModelDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Class for loading/saving MTBTableModel data objects.
MTBTableModelDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
MTBTableModelDataIOSwing.TableModelShowButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: GUI element for displaying table model data.
MTBTableModelDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans: Class for loading/saving MTBTableModel data objects via xmlbeans provider.
MTBTableModelDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBTableModelDataIOXmlbeans
MTBTableWindow - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components: GUI window for displaying tables in MiToBo.
MTBTableWindow(MTBTableModel) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components.MTBTableWindow: Default constructor.
MTBTableWindow.DataTabFileFilter - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components: Internal class that realizes a FileFilter for text files where MiToBo table data is stored.
MTBTermAreaDiff - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination: Check upon snake termination by the area within the snake.
MTBTermAreaDiff() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff: Default constructor.
MTBTermAreaDiff(double, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff: Constructor with area fraction below the snake iteration is terminated or if a maximum number of iterations is reached.
MTBTermAreaDiffSlidingOffset - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination: Check upon snake termination by area change within the snake.
MTBTermAreaDiffSlidingOffset() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset: Default constructor.
MTBTermAreaDiffSlidingOffset(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
MTBTermination - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination: Class for checking termination criteria of the current snake iteration.
MTBTermination() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
MTBTermMaxIterations - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination: Check upon snake termination by a given number of maximal iterations of the snake.
MTBTermMaxIterations() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations: Default constructor.
MTBTermMaxIterations(int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations: Constructor with maximum number of iterations on which the snake optimization is terminated.
MTBTermMotionDiff - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination: Check on snake termination by motion difference.
MTBTermMotionDiff() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff: Default constructor.
MTBTermMotionDiff(double, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff: Constructor with motion fraction factor and maximum iteration count.
MTBtoC2D(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper: Converts a MiToBo polygon to C2D data type.
MTBTopologicalNumber - Class in de.unihalle.informatik.MiToBo.topology: An abstract class to compute topological numbers given a neighborhood.
MTBTopologicalNumber() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
MTBTopologicalNumber.PixelIndexIterator - Class in de.unihalle.informatik.MiToBo.topology
MTBTopologicalNumber.PixelOffsetIterator - Class in de.unihalle.informatik.MiToBo.topology
MTBTopologicalNumber.Point3D - Class in de.unihalle.informatik.MiToBo.topology: This class is used as a light weight 3D point implementation
MTBTopologicalNumber2D - Class in de.unihalle.informatik.MiToBo.topology: An abstract class to compute topological numbers for the 2D case.
MTBTopologicalNumber2D() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2D
MTBTopologicalNumber2DN4 - Class in de.unihalle.informatik.MiToBo.topology: Class to compute topological numbers for the 2D case.
MTBTopologicalNumber2DN4() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN4: Construct a class for this neighborhood definitions
MTBTopologicalNumber2DN8 - Class in de.unihalle.informatik.MiToBo.topology: Class to compute topological numbers for the 2D case.
MTBTopologicalNumber2DN8() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN8: Construct a class for this neighborhood definition
MTBTree - Class in de.unihalle.informatik.MiToBo.core.datatypes: This class implements a simple tree data structure.
MTBTree(MTBTreeNodeData) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree: Constructor for the tree.
MTBTree(MTBTreeNode) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree: Constructor for the tree for a given root node.
MTBTreeNode - Class in de.unihalle.informatik.MiToBo.core.datatypes: This class implements the nodes of class 'Tree'.
MTBTreeNode(MTBTreeNodeData) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: Constructor for a TreeNode.
MTBTreeNodeData - Class in de.unihalle.informatik.MiToBo.core.datatypes: Abstract class to define properties for data objects associated with TreeNodes.
MTBTreeNodeData() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
MTBTreeNodeRegion2D - Class in de.unihalle.informatik.MiToBo.core.datatypes: Class to create a TreeNodeData object for a 2D region (MTBRegion2D).
MTBTreeNodeRegion2D(MTBRegion2D) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D: Construct a new MTBTreeNodeRegion2D from the given 2D region object.
MTBVectorField2D - Class in de.unihalle.informatik.MiToBo.core.datatypes: Class to represent several kinds of vector fields.
MTBVectorField2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
MTBVectorField2D(double[], double[], int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
MTBVersionProviderReleaseFile - Class in de.unihalle.informatik.MiToBo.core.operator: Info class which provides MiToBo plugins with version information from release file in a jar archive.
MTBVersionProviderReleaseFile() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
MTBWrapperDataIOCmdline - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline: Class for loading/saving primitive datatypes in Alida.
MTBWrapperDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBWrapperDataIOCmdline
MTBWrapperDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Class for loading/saving wrapper datatypes in MiToBo.
MTBWrapperDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBWrapperDataIOSwing
MTBWrapperDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans: Class for loading/saving primitive datatypes in Alida.
MTBWrapperDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBWrapperDataIOXmlbeans
mu - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE: weight of the length term
mu - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE: weight of the length term
mu - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Distribution of the number of clutter observations
mult(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Multiply each image value by a constant
mult(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Multiply the elements of two images
mult(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Multiply each image value by a constant
mult(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Multiply the elements of two images
MultiChannelParticleAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.particles2D: Operator for detecting sub-cellular structures in a given image.
MultiChannelParticleAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Empty constructor.
MultiChannelParticleAnalyzer2D(MTBImage, Vector<ParticleDetector>) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Default constructor.
MultiChannelParticleAnalyzer2D.ResultImageMode - Enum in de.unihalle.informatik.MiToBo.apps.particles2D: Display mode of the result image.
MultiObsDistributionIndepGaussians<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl: A simple multi observation density, which assumes independence of the single observations with multivariate Gaussian noise.
MultiObsDistributionIndepGaussians(Random, Matrix, Matrix, AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
MultiObsDistributionIndepGaussians(Random, Matrix[], Matrix[], AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
MultiObsDistributionIndepGaussians(Random, Matrix, Matrix, MultiStateDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
MultiObsDistributionIndepGaussians(Random, Matrix[], Matrix[], MultiStateDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
MultiObsDistributionIndepGaussians(Random, Matrix, Matrix, MultiStateLinTransDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
MultiObsDistributionIndepGaussians(Random, Matrix[], Matrix[], MultiStateLinTransDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
MultiObsDistributionIndepGaussMix<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl: A simple multi observation density, which assumes independent Gaussian mixtures as the underlying distributions.
MultiObsDistributionIndepGaussMix(Random, Matrix, Vector<GaussMixDistribution>, AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
MultiObservationGenerator - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo: Operator to create a (time) series of observations which can be used for evaluation of multi target tracking algorithms.
MultiObservationGenerator() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
MultiObservationGenerator.GeneratorInfo - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
MultiObservationTrackerRBMCDAIMM - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo: Tracking of multiple targets using Rao-Blackwellized Monte Carlo Data Association (RBMCDA) for observation-to-target association and Interacting Multiple Models (IMM) filters for target state estimation.
MultiObservationTrackerRBMCDAIMM() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
multiphase - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
MultiState<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl: Multi-target state implementation.
MultiState(MultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
MultiStateDistributionIndepGaussians<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl: A simple multi state density, which assumes independence of the single states with multivariate Gaussian noise.
MultiStateDistributionIndepGaussians(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
MultiStateDistributionIndepGaussians(AbstractMultiState<T>, Matrix, Random) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians: Constructor with identical covariance matrices for all states
MultiStateDistributionIndepGaussians(AbstractMultiState<T>, Vector<Matrix>, Random) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians: Constructor with different covariance matrix for each state
MultiStateFactory<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl: Multi-target state factory implementation.
MultiStateFactory(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiStateFactory
MultiStateIO - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatools: File-IO for (vectors of) MultiState objects.
MultiStateIO() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.MultiStateIO
MultiStateLinTransDistributionIndepGaussians<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl: A simple multi state-transition density, which assumes independence of the single states and multivariate Gaussian process noise.
MultiStateLinTransDistributionIndepGaussians(Random, Matrix, Matrix, AbstractMultiState<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
MultiStateLinTransDistributionIndepGaussians(Random, Matrix[], Matrix[], AbstractMultiState<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
MultiStateLinTransDistributionIndepGaussians(Random, Matrix, Matrix, MultiStateDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
MultiStateLinTransDistributionIndepGaussians(Random, Matrix[], Matrix[], MultiStateDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
MultiTargetIMMFilter - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo: Multi-target Interacting Multiple Models (IMM) filter for varying number of targets.
MultiTargetIMMFilter(MultiTargetIMMFilter) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter: Copy constructor.
MultiTargetIMMFilter(Vector<GaussMixDistribution>, LinearTransformGaussNoise, LinearTransformGaussNoise[], Matrix, double, ExponentialDistribution, GaussMixDistribution, Matrix, AbstractMultiStateFactory<MotionModelID>, AbstractMultiStateFactory<MotionModelID>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter: Constructor that initializes the internal random generator with seed 1.
MultiTargetIMMFilter(Vector<GaussMixDistribution>, LinearTransformGaussNoise, LinearTransformGaussNoise[], Matrix, double, ExponentialDistribution, GaussMixDistribution, Matrix, AbstractMultiStateFactory<MotionModelID>, AbstractMultiStateFactory<MotionModelID>, Random) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter: Constructor.
MultiTargetPredictionFilter<T extends Copyable<?>> - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.algo: Interface for multi-target prediction filters
MultiTargetPredictionFilterIndep<T extends Copyable<?>> - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.algo: Interface for multi-target prediction filters with independent targets
MultiTargetRBMCDA<T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo: Rao-Blackwellized Monte Carlo Data Association following:
S.
MultiTargetRBMCDA(Random, RBMCDASample<T>, int, AssociationDistribution<T, T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
MultiTargetRBMCDA(Random, RBMCDASample<T>[], AssociationDistribution<T, T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
myClass - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
myClass - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel: Class associated with parameter.
myClass - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
myData - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
myDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
myDescriptor - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel: Descriptor associated with parameter.
myField - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
myField - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel: Field associated with parameter.
myField - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
myObject - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel: (Default) object value associated with parameter.
myX - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: The flows of the field in x- and y-direction.
myY - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: The flows of the field in x- and y-direction.

N

n - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: For Odet's criteria only
n - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria: Exponent for calculations.
n - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
n - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelIndexIterator
n - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
N - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution: number of targets
naiveGapThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Maximal distance of gaps in naive mode to be closed.
name - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
name - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Name of the energy.
narrow - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Pixels in narrow-band.
narrowBandWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
naString - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
nbMode - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal: Neighborhood(s) to be considered.
nbPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
nbPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Phases of the 8-neighbors of the current pixel.
nbPhasesNonredundant - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Non redudant phases in the neighborhood of the current pixel.
nColors - Variable in class de.unihalle.informatik.MiToBo.color.tools.DistinctColorListGenerator: Number of colors to generate.
nearZero(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Checks if a pixel belongs to the zero level.
negDir - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
NeighborhoodSelection() - Constructor for enum de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal.NeighborhoodSelection
neighbourhood - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: The neighbourhood mode to inspect new pixel.
neighbourhood - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
neighbourhood - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: The neighbourhood mode to inspect new pixel.
Neighbourhood() - Constructor for enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.Neighbourhood
neurite - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
neuriteColor - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
neuriteColor - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Region color of detected neurites to view the neurites in the result image.
neuriteDetection(MTBContour2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Main method for 2D neurite detection.
neuriteDetector - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Define analyzer parameters.
NeuriteDetector2D - Class in de.unihalle.informatik.MiToBo.apps.neurites2D: The Neurite Detector 2D application offers advanced functionality to detect neurites in 2D fluorescence microscope images of neurons.
NeuriteDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Standard constructor.
NeuriteDetector2D(String, Integer, int, double, Integer[], double, int, NeuriteDetector2D.NeuriteDetector2DMode, NeuriteDetector2DAlgos.DetectorExternalEnergy, double, double, double, double, int, int, int, int, Color, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Constructor
NeuriteDetector2D.NeuriteDetector2DMode - Enum in de.unihalle.informatik.MiToBo.apps.neurites2D: Different detection modes.
NeuriteDetector2DAlgos - Class in de.unihalle.informatik.MiToBo.apps.neurites2D: The class implements the basic algorithm for neurite detection based on a 2D multichannel fluorescence image.
NeuriteDetector2DAlgos() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Standard constructor.
NeuriteDetector2DAlgos(MTBImage, int, int, double, int[], double, int, String, String, NeuriteDetector2DAlgos.DetectorExternalEnergy, double, double, double, double, int, int, int, int, Color, MTBTableModel, Boolean, Rengine) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Constructor.
NeuriteDetector2DAlgos.DetectorExternalEnergy - Enum in de.unihalle.informatik.MiToBo.apps.neurites2D: Label for different external energies of the snake which can be used by the detector.
NeuriteDetector2DException - Exception in de.unihalle.informatik.MiToBo.apps.neurites2D: Exception handling for 2D neurite detection.
NeuriteDetector2DException() - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DException
NeuriteDetector2DException(String) - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DException
NeuriteDetector2DMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D.NeuriteDetector2DMode
NeuriteExtractor2D - Class in de.unihalle.informatik.MiToBo.apps.neurites2D: The Neurite Extractor 2D application offers advanced functionality to extract neurite regions in 2D binary neuron images of neurons.
NeuriteExtractor2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Standard constructor.
NeuriteExtractor2D(MTBImageByte, NeuriteExtractor2D.NeuronColor, int, int, Rengine, String) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Constructor to create a new neurite extraction object.
NeuriteExtractor2D.NeuronColor - Enum in de.unihalle.informatik.MiToBo.apps.neurites2D: Color of binary neuron image foreground.
NeuriteExtractor2DException - Exception in de.unihalle.informatik.MiToBo.apps.neurites2D: Exception handling for 2D neurite extraction.
NeuriteExtractor2DException() - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2DException
NeuriteExtractor2DException(String) - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2DException
neuriteGraph - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Neurite skeleton Graph (NSG) of the current neurite.
neuriteGraphs - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Vector of neurite graphs, one for each localized neurite.
neuriteMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
neuriteMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Mask size of average neurite with in pixel.
neuriteMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
NeuriteMolProfExtractor2D - Class in de.unihalle.informatik.MiToBo.apps.neurites2D: The Neurite Molecular Profile Extractor 2D application offers advanced functionality to extract molecular intensity profiles of multichannel fluorescence images along detected neurite regions.
NeuriteMolProfExtractor2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D: Standard constructor
NeuriteMolProfExtractor2D(MTBImage, Integer[], MTBNeurite2DSet, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D: Constructor to create a new neurite profile extraction operator.
NeuriteParticleDetector2D - Class in de.unihalle.informatik.MiToBo.apps.neurites2D: This operator detects particles of a neuron image, for example from FISH analysis.
NeuriteParticleDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D: Standardconstructor.
NeuriteParticleDetector2D(Integer, ParticleDetectorUWT2D, MTBNeurite2DSet, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D: Constructor.
neuriteProfiles - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: The current list of the neurite profiles.
neuriteRegion - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Neurite corresponding region as MTBRegion2D object.
neuriteSet - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
neuriteSet - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D: Set of neurite regions for detecting particle only inside these regions, an be null for detection all particles in the complete image
neuriteSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet: The current set of neurites.
neuriteShaft - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Neurite corresponding neurite shaft region as MTBRegion2D object.
neuriteShaftLengths - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Array of detected lengths of the neurite shafts, without growth cone regions.
neuriteShaftLengths - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Lengths of the single branches of a neurite shaft.
neuriteWidths - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Average widths of the whole neurite, the neurite shaft and the growth cone.
NeuronAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.neurons2D: The Neuron Analyzer 2D application offers advanced functionality to analyze 2D fluorescence microscope images of neurons.
NeuronAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Standard constructor.
NeuronAnalyzer2D(NeuriteDetector2D, Boolean, String[], Integer[], Boolean, NeuriteParticleDetector2D, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Constructor.
NeuronAnalyzer2DException - Exception in de.unihalle.informatik.MiToBo.apps.neurons2D: Exception handling for 2D neuron analyzer.
NeuronAnalyzer2DException() - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2DException
NeuronAnalyzer2DException(String) - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2DException
neuronChannels - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
neuronChannels - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Channel numbers, including the neuron stains for detection of the neurons in the current multichannel fluorescence image.
neuronCoarseSoma - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: 2D region of the coarse cell body region (soma).
neuronColor - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
NeuronColor() - Constructor for enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D.NeuronColor
neuronImage - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Define extractor parameters.
neuronMIP - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Maximum intensity projection (MIP) image of the neuron.
neuronSkelGraph - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: NSG of the whole neuron.
newborndistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution: spatial distribution of observations from newborn targets
newbornStateDistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
newbornStateFromObs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
newtargetID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Target-ID to start from for newborn targets
next() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
next() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
next() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
next() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
next - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
next() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelIndexIterator
next() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
nextSegment - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Reference to the subsequent segment along the contour.
nf - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
nf - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
nf - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
niblackConstant - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
niblackConstant - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Application based constant for Niblack thresholding.
niblackOperator - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Niblack operator, required if mode is 'NIBLACK'.
niblackVarianceThresh - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Niblack threshold.
nInitialTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
noCheck - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
Node - Class in de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation
Node() - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
Node(double, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
Node(int, double, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
Node(int, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
node - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData: Reference to the associated node of the tree.
nodeID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID: The node's ID
nodeIsSrc(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
nodeIsTgt(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
nodeNames - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
nodes - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Vector of included graph nodes.
nodes - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
nodeThreshold - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Threshold for nodes to be included, nodes with an intensity above the threshold are removed from the graph.
nodeType - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode: MTBSkeletonNodeType of the MTBSkeletonGraphNode.
noiseCov - Variable in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
noNeighborsOldAlgo - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
nonProtrusionArea - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Non-protrusion area in cell region.
nonProtrusionAreas - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
normalizationFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Normalization factor for scaling matrix entries.
normalizationFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Normalization factor for scaling matrix entries.
normalizationFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Normalization factor for scaling matrix entries.
normalize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: Normalize the histogram.
normalize(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Normalizes the snake coordinates.
normalizedFilterResponse(double, double) - Static method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Computes the (ideal) filter response to the Gaussian derivative kernel.
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance: Normalize the external energy in a range [0.0, 1.0].
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D: Normalization of the GVF field. !!!
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity: Normalize the external energy in a range [-1.0, 1.0].
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Normalize the external energy in a range [-1.0, 1.0].
normalizeImplicitParameters() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Normalizes the implicit parameters so that f=1.0.
normalizeInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Normalizes image intensities according to normalization mode of operator.
normalizeMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D: Flag to normalize sum of kernel elements to zero.
normalizeMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D: Flag to normalize sum of kernel elements to zero.
normalizeMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Flag to normalize sum of kernel elements to zero.
normalizePotentialToMin(double[], boolean) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder: Function to normalize a potential to the minimum value of 0.
normalizeWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution: Normalize weights
normalizeWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Normalize the particle weights to sum to 1.
normfactor - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution: normalization factor
normFromTo(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
normImageFromTo(MTBImage, double, double, double, double, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools: Normalize the image values to range [lowerBound, upperBound].
normImageTo(MTBImage, double, double, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools: Normalize the image values to range [lowerBound, upperBound].
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Mode of normalization.
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Mode of normalization.
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Mode of normalization.
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Mode of normalization.
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Mode for normalizing energies.
normTo(MTBImage, double, double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
normValues() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Normalize the values in the gvf field in a range of [-1,1].
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
nrs - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
nTimesteps - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
nu - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE: weight of the size term
nu - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE: weight for this energy
nu - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Distribution of the number of observations from newborn targets
nucChannel - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
nucDetector - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
nucImage - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Part of the input image, representing the stained nuclei.
NuclDetectMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D.NuclDetectMode
NuclearParticleDetector2D - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D: This class detects nuclei and particles inside these nuclei and gives some statistics about particles, like particle number per nuclei, particle size, sum of intensities, etc.
NuclearParticleDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Standard constructor.
NuclearParticleDetector2D(MTBImageByte, Integer, Integer, Boolean, Double, Boolean, NucleusDetector2D, ParticleDetectorUWT2D) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
nucleiChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Nuclei channel.
nucleiChannel - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
nucleiChannel - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Channel number, including the nuclei, in the current multichannel fluorescence image.
nucleiContours - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: (Optional) initial snake contours for nuclei.
nucleiDetector - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Operator for nucleus detection/separation.
nucleiMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Nuclei mask.
nucleiRegions - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Set of detected regions.
nucleiRegions - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
nucleus - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Fluorescence labeled nuclei image from the multichannel microscope image.
nucleusChannelID - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Index of the nucleus channel, if -1 it is unknown or image has only one.
NucleusDetector2D - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D: Operator for segmenting cell nuclei in 2D images.
NucleusDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Default constructor.
NucleusDetector2D(MTBImage, NucleusDetector2D.NuclDetectMode, ImgThreshNiblack, boolean, int, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Constructor.
NucleusDetector2D.NuclDetectMode - Enum in de.unihalle.informatik.MiToBo.apps.nuclei2D: Available modes for nuclei segmentation in 2D images.
nucleusRatio - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
nucleusRatio - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Ratio of nucleus pixels which should be included in a intact neuron region to specify the neuron region as active and use for detection.
nucleusResult - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Result for nucleus channel.
NucleusSeparator2D - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D: Class provides routines for separating conglomerates of cell nuclei in 2D.
NucleusSeparator2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D: Empty constructor.
NucleusSeparator2D(MTBImage, NucleusSeparator2DAlgos) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D: Default constructor.
NucleusSeparator2D.ResultImageMode - Enum in de.unihalle.informatik.MiToBo.apps.nuclei2D: Display mode of the result image.
NucleusSeparator2DAlgos - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D: Common super class for all nucleus separators.
NucleusSeparator2DAlgos() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos: Empty constructor.
NucleusSeparator2DBeamCut - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D: Class provides routines for separating conglomerates of cell nuclei in 2D.
NucleusSeparator2DBeamCut() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Default constructor
NucleusSeparator2DBeamCut(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Constructor.
NucleusSeparator2DBeamCut(MTBImage, NucleusSeparator2DBeamCut.NuclSeparateMode) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Constructor.
NucleusSeparator2DBeamCut.NuclSeparateMode - Enum in de.unihalle.informatik.MiToBo.apps.nuclei2D: Available modes for nuclei separation in 2D images.
NucleusSeparator2DPeakSearch - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D: Operator for separating merged nuclei regions in images.
NucleusSeparator2DPeakSearch() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Default constructor.
NucleusSeparator2DPeakSearch(MTBImageShort) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Constructor with input image.
NucleusSeparator2DPeakSearch(MTBImageShort, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Constructor with gray-scale and binary image.
NucleusSeparator2DPeakSearch_RegionSeparator - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D: Operator to analyze a given binary image or a set of nuclei regions.
NucleusSeparator2DPeakSearch_RegionSeparator() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Default constructor.
NucleusSeparator2DPeakSearch_RegionSeparator(MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Constructor with input image.
NucleusSeparator2DPeakSearch_RegionSeparator(MTBRegion2DSet) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Constructor with region set.
nucleusSepOp - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Operator to be applied for nuclei separation.
nucleusSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
nucleusSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Minimum size of nucleus region to set region as intact nucleus.
NuclSeparateMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut.NuclSeparateMode
nucSepOp - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D: Operation mode of the operator.
number_cells - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Count of detected cells.
number_channels - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Number of channels in the image.
number_nuclei - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Count of detected nuclei.
number_particles - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Count of detected particles.
numberNeighbors - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Number of neighboring pixels to consider for LBP codes.
numberOfBins - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
numberOfEdges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Number of edges in the MTBGraph.
numberOfNeighbors(MTBImage, int, int) - Static method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Counts the number of neighboring skeleton pixels.
numberOfNeighbors(MTBImage, int, int) - Static method in class de.unihalle.informatik.MiToBo.morphology.SkeletonAnalysisHelper: Counts the number of neighboring skeleton pixels.
numberOfNodes - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Number of nodes in the MTBGraph.
numberOfProtrusions - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: Number of detected protrusions along contour.
numberToString(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
numBlockChange(short[], int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Return number of connected components of different/foreign phase then r in the 8 neighborhood nbPhases, which are 4 connected to the current pixel.
numClutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
numClutterInput - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult: number of clutter observations in input observations
numClutterTracker - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult: number of clutter observations in tracking results
numDeadTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
numEntries - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: number of histogram entries
numInitialTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
numIterations - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
numIterations - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
numIterations - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Number of iterations for calculating the GVF field.
numIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
numIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
numIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
numNewbornTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
numObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
numOfConnectedNodes(PartitGraphNodeID, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning: Get number of nodes from partition 'partitionID' connected to current node
numOfDefinedHuePixel - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
numOfDefinedSaturationPixel - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
numOfNodes() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
numOfNodes() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix: Get number of graph nodes
numOfObservationAssocs(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
numOfObservationAssocs(int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation: Get the number of observations that are associated with the specified target
numOfTargetAssocs(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
numOfTargetAssocs(int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation: Get the number of targets that are associated with the specified observation
numOfXPixel - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
numPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE: number of phases including background
numPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
numPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
numRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Number of represented regions.
numRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: Number of represented regions.
numSamples - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
numTargetInput - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult: number of target observations in input observations
numTargetTracker - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult: number of target observations in tracker results
nx - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Used for drawing the estimated diameter during Ridge Detection.
nx - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
ny - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Used for drawing the estimated diameter during Ridge Detection.
ny - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node

O

obj - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowButton: Image object associated with the button.
objectLabels - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
objects26Connected - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
objects8Connected - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
objects8Connected - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
obsAssocAdjacency - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
obsConflict(Matrix, MultiState<MotionModelID>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
ObsDistance(double, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ObsDistance
obsdistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution: observation/measurement likelihood P(z_m^t | c_m, Z^{1:t-1}, c_{1:m-1}
obsDomainAreaRatio - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
ObservationAdjacency - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl: An adjacency matrix for observations in a time series used for greedyGourmet-partitioning.
ObservationAdjacency(Vector<MultiState<MotionModelID>>, RBMCDASampleInfo<MotionModelID>[]) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency: Constructor that initializes the adjacency matrix with the given observations and sets edge weights according to the information from RBMCDA-samples
ObservationAdjacency(Vector<MultiState<MotionModelID>>, DataAssociationExclusive[][]) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency: Deprecated.
ObservationAdjacency(ObservationAdjacency) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
observations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
observations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
observations - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
ObservationSeriesGenerator - Class in cmdTools.tracking.multitarget: Commandline tool to create a (time) series of observations which can be used for evaluation of multi-target tracking algorithms.
ObservationSeriesGenerator() - Constructor for class cmdTools.tracking.multitarget.ObservationSeriesGenerator
ObservationsInfo - Class in cmdTools.tracking.multitarget: Commandline tool to print information about a (time) sequence of observations and optionally their association to targets/clutter.
ObservationsInfo() - Constructor for class cmdTools.tracking.multitarget.ObservationsInfo
observationsToRegions(boolean, Vector<MultiState<MotionModelID>>, double, double, double, double) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter: Convert observations to regions.
observationsToTracks(Vector<MultiState<MotionModelID>>, HashMap<Integer, Vector<Integer>>) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter: Obtain observations assigned to each target from observations with assigned target IDs
obsIdx - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ObsDistance
OCO(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria: This method implements Odet's oversegmentation error.
OCU(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria: This method implements Odet's undersegmentation error.
ODE(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors: This method computes the overdetection error.
Odet - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Check if you want to compute Odet's criteria
offer(EType, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList: add an element to List
offsets - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
offsetsNeighborNeighbors - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: As for the neighbors this collection is in analogy to coordinatesNeighborNeighbors and gives for each neighborneighbor the offset instead of coordinates.
offsetsNeighbors - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: In analogy to coordinatesNeighbors this array hold the offsets of the neighbors.
oFilter - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Oriented filter to apply.
okOption - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Ok label to be used on button of Ok message boxes.
oldId - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D: Old index (position) of the point within the snake.
omemeta - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
omePixelType(MTBImage.MTBImageType) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils: Get the OME pixel type corresponding to the specified MTB image type
omexml - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
omitAssignment - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Flag to omit region assignment.
onValue - Static variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
op - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

The operator associated with this frame.
opane - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane.FileOptionsRefresher
open(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
open1D(double[], int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
openByteImageWithCircle(MTBImage, int) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Open an image of type MTBImageByte.
openingSESize - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: The minimum size of a MTBRegion2D before erosion.
openingSESize - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: The minimum size of a MTBRegion2D before erosion.
openRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Gets an instance of the current ROI manager of ImageJ.
openRoiManagerFile(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Opens a zip file with ImageJ ROIs.
openWindow() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Displays configuration window.
openWindow() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Displays configuration window.
openWindows - Static variable in class cmdTools.visualization.DisplayImage
operate() - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
operate() - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Invokes analysis procedure on given image.
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
operate() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetector
operate() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT
operate() - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
operate() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
operate() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
operate() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
operate() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
operate() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
operate() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
operate() - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter
operate() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
operate() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Creates a MTBImage with three channels, the same size as the original one and converts each rgb pixel to a hsx pixel, where x stands for Inentsity or Brightness or Value depending on the mode set.
operate() - Method in class de.unihalle.informatik.MiToBo.color.tools.DistinctColorListGenerator: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
operate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
operate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
operate() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter
operate() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
operate() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
operate() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
operate() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
operate() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
operate() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
operate() - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
operate() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats
operate() - Method in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
operate() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
operate() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
operate() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
operate() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
operate() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression
operate() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: This function calls the actual Gauss filtering method.
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: This function calls the actual mean filtering method.
operate() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
operate() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
operate() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
operate() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
operate() - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
operate() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
operate() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
operate() - Method in class de.unihalle.informatik.MiToBo.io.importer.GetMTBContour2DSetFromXSVFiles
operate() - Method in class de.unihalle.informatik.MiToBo.math.arrays.filter.GaussFilterDouble1D: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet
operate() - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet
operate() - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
operate() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
operate() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
operate() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
operate() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.WatershedBinary
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: This method initializes all required components.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: This function does the actual work, i.e. optimization of the energy.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Methode that runs the operator.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
operate() - Method in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.CropImage
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
operate() - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
operate() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
operate() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
operate() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
operate() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
OperationMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.OperationMode
OperationMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D.OperationMode
OperationMode() - Constructor for enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap.OperationMode
OperationMode() - Constructor for enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping.OperationMode
operationType - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: The operation which should be applied to the input vector field.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Identifier string for this operator class.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Identifier string for this operator class.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Identifier string for this operator class.
operatorID - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Identifier string for the operator class.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter: Identifier string for this operator.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter: Identifier string for this operator.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Identifier string for this operator class.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Operator class identifier.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Identifier string for this operator class.
operatorMode - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Mode of operation of the operator.
OperatorPhasesToRun() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.OperatorPhasesToRun
opID - Static variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor: Identifier string for this operator class.
opID - Static variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor: Identifier string for this operator class.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Identifier for outputs in verbose mode.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Identifier for outputs in verbose mode.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Identifier for outputs in verbose mode.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT: Identifier for outputs in verbose mode.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules: Identifier for outputs in verbose mode.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: Identifier for outputs in verbose mode.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Identifier for outputs in verbose mode.
opMode - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Mode of operation of the operator.
opMode - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Detection mode.
opMode - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Operation mode of this separator.
opMode() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.opMode
opMode - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Mode of operation of the operator.
opMode - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Mode of operation of the operator.
opName - Variable in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorDocumentationFrame: Name of associated operator.
opPackage - Variable in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorDocumentationFrame: Package of associated operator/tool.
optimizeContrast(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Optimize visibility by shifting labels into upper part of gray-scale range.
optimizer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate: Current snake optimizer with all its parameters and fields like the current snake, old snake, gamma values and energies.
optimizer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination: Current snake optimizer with all its parameters and fields.
optimizeSnakes(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Optimization of the snakes (main snake and inner snakes) with its specified parameters and energies.
OpWorkingMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator.OpWorkingMode
or(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Bitwise OR of the elements of two images
or(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Bitwise logical OR of two images.
ordinalToType(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Return the corresponding MTBImageType for its index in the enum.
orient - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: List of orientations of plastid regions.
orientation - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
orientation - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
orientation - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Ellipse orientation in degrees.
OrientedFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic: Base class for anisotropic linear filters in 2D.
OrientedFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D: Default constructor.
OrientedFilter2D.ApplicationMode - Enum in de.unihalle.informatik.MiToBo.filters.linear.anisotropic: Modes how to apply the filter to an image.
OrientedFilter2DBatchAnalyzer - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic: Base class for applying oriented filters in different orientations.
OrientedFilter2DBatchAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Default constructor.
OrientedFilter2DBatchAnalyzer.JoinMode - Enum in de.unihalle.informatik.MiToBo.filters.linear.anisotropic: Method for joining the results from the various orientations.
originalImage - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Original image currently under processing.
ostream - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
out - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.WriteXML
outdata - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
outDigits - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
outDigits - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
outDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Output and working directory.
outDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Output and working directory.
outEdges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Vector of outgoing edges of the MTBGraphNode.
outFile - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
outFile - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter: Output file name.
outImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker: Output image.
outImageType - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
OutImageType() - Constructor for enum de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB.OutImageType
outimg - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
outImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Binary result image.
outImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Result image.
outIntermediateResultsStack - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Image stack with intermediate result images.
outIntermediateResultsStackInterval - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Interval for saving intermediate results in stack.
outIntermediateResultsStackWanted - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Flag to request a stack of intermediate result images.
outMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker: Generated mask.
outModes - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
outOfRangeValueMode - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Mode how to handle values out of range and masked pixels.
OutOfRangeValuesHandlingMode() - Constructor for enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap.OutOfRangeValuesHandlingMode
outpath - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Directory of output results.
outputArray - Variable in class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D: Result data array.
outputData - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
outputDir - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Directory of output results.
outputDir - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
outputDir - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Optional output directory.
outputEntropy - Variable in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization: Final Shannon entropy of the output image.
outputImage - Variable in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
outputImage - Variable in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
outputImage - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
OutputMode() - Constructor for enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.OutputMode
outputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
outputPath - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter: Path where to save the tile files.
outputSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner
outputType - Variable in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
outputType - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
outRegs - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
outSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter: Result snake.
outSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter: Resulting snake.
outSnakes - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter: Result snakes.
outSnakes - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Result contours.
outSnakesImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Image with final snake contours overlayed.
overlapMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Current overlap mask for joint optimization of multiple snakes.
overlapMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Mask to indicate overlap regions between snakes.
overlapMaskRequested - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Flag to indicate if overlap mask is required by at least one energy.
overlapOpt - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Mode for how to resolve overlaps of lines.
overwrite - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
OverwriteException - Exception in de.unihalle.informatik.MiToBo.io.images: Special exception for the ImageWriterMTB operator.
OverwriteException(ALDOperatorException.OperatorExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.io.images.OverwriteException

P

P(Double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
p(Integer) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
p(Integer) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
p - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
p(T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.EvaluatableDistribution: Evaluate p(X) at location x.
p(T, int) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.IndependentlyEvaluatableDistribution: Evaluate p_i(X) at x_i
P(T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.IntegrableDistribution: Evaluate probability distribution function P(X <= x)
p(AbstractMultiState<S>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
p(AbstractMultiState<S>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep: Evaluate the density independently for observation i in Z conditional on state j in X
p(AbstractMultiState<S>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep: Evaluate the density independently for observation i in Z conditional on state i in X
p(AbstractMultiState<S>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
p(DataAssociation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: This method is here only valid for the latest DataAssociation sampled with drawSample().
p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
p(AbstractMultiState<T>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
p(AbstractMultiState<T>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
P_D - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution: Probability of target detection
p_obs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
P_t - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: The final transformation matrix to be used for dimension reduction.
PaCeQuant - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology: Operator for segmenting and analyzing pavement cell shape.
PaCeQuant() - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Default constructor.
PaCeQuant.BorderBackgroundContrast - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology: Border color.
PaCeQuant.GapCloseMode - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology: Heuristic for closing border gaps.
PaCeQuant.ImageType - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology: Image type.
PaCeQuant.LobeTypes - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology: Different types of lobes.
PaCeQuant.MeasurementUnits - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology: Unit for measurements.
PaCeQuant.OperationMode - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology: Operation mode of the operator.
PaCeQuant.OperatorPhasesToRun - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology: Phases to run.
PaCeQuant.PixelCalibration - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology: Mode of calibrating pixel size.
PaCeQuant.SegmentationInputFormat - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology: Formats for input of external segmentation results.
PaCeQuant.SegmentationResult - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology: Internal class for representing the result data of segmenting an image.
PaCeQuant.SkeletonPostprocessor - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology: Helper operator to post-process border skeletons.
PaCeQuant_FeatureColorMapperInputData - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology: Datatype to handle input configurations for PaCeQuant_FeatureColorMapper.
PaCeQuant_FeatureColorMapperInputData(String, int[]) - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputData: Default constructor.
PaCeQuant_FeatureColorMapperInputDataIOSwing - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology: Data I/O provider for input data of PaCeQuant_FeatureColorMapper.
PaCeQuant_FeatureColorMapperInputDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing
PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology: Panel for handling GUI I/O of input directories for PaCeQuant_FeatureColorMapper.
PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology
paintComponent(Graphics) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
paintFilledRegion(MTBRegion2D, MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: Draw a region without holes to an image.
paintFilledRegionsBinary(MTBImage, MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: Close holes in binary image.
paintZeroWeightEdges - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
panelContainer - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel: Main panel containing all graphical components.
param - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
paramDescr - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
paramDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: (Operator) parameter descriptor associated with parameter.
paramDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel: (Operator) parameter descriptor of associated parameter.
paramDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
paramDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage: (Operator) parameter descriptor of associated parameter.
paramDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton: Descriptor of underlying parameter.
paramDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser: (Operator) parameter descriptor of associated parameter.
paramDescr - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: (Operator) parameter descriptor of associated parameter.
paramDescriptor - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel: Descriptor of the associated (operator) parameter.
parent - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: Parent node
parentID - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtColorDataIOCmdline: A java.awt.Color object is created from a string, which holds color information in the following format:

"rINT:bINT:gINT[:aINT]"

where INT is an integer value in the range [0,255].
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtPoint2dDataIOCmdline: A java.awt.geom.Point2D.Double object is created from a string, which holds coordinates in the following format:

"x;y" "rINT:bINT:gINT[:aINT]"

where INT is an integer value in the range [0,255].
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBWrapperDataIOCmdline: Method to parse MTB wrapper data from a string.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.RandomGeneratorDataIOCmdline: Convert a string to a Random generator.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
partChannel - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
partDetector - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
particleChannel - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D: Define extractor parameters.
particleDetector - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Particle detector.
particleDetector - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
particleDetector - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
ParticleDetector - Class in de.unihalle.informatik.MiToBo.apps.particles2D: Common super class for all particle detectors.
ParticleDetector() - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetector: Empty constructor.
ParticleDetector2D - Class in cmdTools.cellAnalysis: Commandline tool for particle detection based on the undecimated wavelet transform.
ParticleDetector2D() - Constructor for class cmdTools.cellAnalysis.ParticleDetector2D
particleDetector_1 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
particleDetector_2 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
particleDetector_3 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
particleDetector_4 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
particleDetector_5 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
ParticleDetectorUWT2D - Class in de.unihalle.informatik.MiToBo.apps.particles2D: Detector for spotlike structures (bright on dark background) in 2D based on the undecimated wavelet transform.
ParticleDetectorUWT2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Constructor.
ParticleDetectorUWT2D(MTBImage, int, int, double, int, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Constructor with non-default parameters.
ParticleDetectorUWT2D(MTBImage, int, int, double, int, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Constructor that sets the poisson2gauss flag to true
ParticleDetectorUWT2D.UWTRunner - Class in de.unihalle.informatik.MiToBo.apps.particles2D: Thread class to run UWT wavelet transformation threaded.
ParticleDistribution<G extends Copyable<? extends G>> - Class in de.unihalle.informatik.MiToBo.math.distributions.impl: A distribution represented by weighted particles
ParticleDistribution() - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Constructor where all fields are initialized by null.
ParticleDistribution(Random, G[]) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Constructor with equally weighted particles that must be specified.
ParticleDistribution(Random, G[], double[]) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Constructor with equally weighted particles that must be specified.
ParticleDistribution(Random, SamplingDistribution<G>, int) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Constructor that samples numParticles from density.
particleOp - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT: Particle detector object.
particleOp - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT: Particle detector object.
particleRegions - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: List of detected regions.
particleRegions - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
particleResults - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Detection results for particles.
particles - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
partImage - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Part of the input image, representing the stained particles.
PartitGraphNodeID - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl: A graph node object for multipartite graphs to store a partitionID, a nodeID as well as a subgraphID.
PartitGraphNodeID(int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID: Constructor to specify partitionID and nodeID (subgraphID=0)
PartitGraphNodeID(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID: Constructor to specify partitionID, nodeID and subgraphID
partitionID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID: The node's partitionID
partitions - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
path - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
path - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
path - Variable in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData: Absolute directory path associated with this node.
pathfield - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
PCA - Class in de.unihalle.informatik.MiToBo.math.statistics: This class implements the Karhunen-Loeve transformation, also known as PCA.
PCA() - Constructor for class de.unihalle.informatik.MiToBo.math.statistics.PCA: Default constructor.
PCA.ReductionMode - Enum in de.unihalle.informatik.MiToBo.math.statistics: Available modes for determining the sub-space dimensionality.
Pdeath - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
pdeath - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
pDetect - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
pDetect - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
pdetector - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
pdfs - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
peakdistance - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
perCellAvgSize - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Average particle size per cell (optional).
perCellCount - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Particle counts per cell (optional).
percentageVar - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Variance fraction for automatic dimension selection in mode ReductionMode.PERCENTAGE_VARIANCE.
perimeters - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
perimeters - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
pgm - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
phaseAInfo - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Info string for segmentation phase configuration parameters.
phaseBInfo - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Info string for segmentation phase configuration parameters.
phasesToRun - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Select with phases to run.
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives: Level set function.
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: The level set function.
phi_0 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
phi_1 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
phi_old - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Variable to store old level set function for comparison with new one.
physicalPixelSize_from_OME(Calibration, IMetadata, int) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils: Set the calibration of an image from the OME meta data of image of index imageIdx
physicalPixelSize_to_OME(Calibration, IMetadata, int) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils: Set OME meta data for image of index imageIdx using information from a Calibration object.
PI_HALF - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
pixCalibMode - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Mode for calibrating physical pixel size.
PixelCalibration() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.PixelCalibration
PixelIndexIterator() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelIndexIterator
pixelLength - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Length of a pixel.
pixelLengthXY - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Physical size of a pixel.
pixelLengthXYinternal - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Pixel length only used internally.
PixelOffsetIterator() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
pixelUnitString - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Unit for pixel length.
PlastidDetector2DParticlesUWT - Class in de.unihalle.informatik.MiToBo.apps.plantCells.plastids: Operator to detect plastid regions in 2D microscope images.
PlastidDetector2DParticlesUWT() - Constructor for class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT: Default constructor.
plastidMarkerType - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules: Type of plastid markers.
plastidMask - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Binary mask of pre-segmented plastid regions.
plastidRegions - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT: Set of detected plastid regions with stromuli.
plastidRegions - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: (Optional) set of detected plastid regions.
plotImageToBackground() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Copies the input image as background into the output frame.
plotSnakesToImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Returns overlay of output snakes onto current input image.
plotSnakesToImage(MTBPolygon2DSet, MTBImage, int[]) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Returns overlay of given snakes onto given image.
plotSnakeToImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
pmf - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution: probability mass function
png - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
pobs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter: observation distribution: independent Gaussian mixtures for each target
point - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.DistanceTargetFunction: Point for which to calculate the distance to the ellipse.
point2DDiff(Point2D.Double, Point2D.Double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Substract two Point2D.Double .
point2DList - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
point2DSum(Point2D.Double, Point2D.Double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Sums up two Point2D.Double .
Point3D(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
PointConfigPanel(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel: Default constructor.
pointHashtableToString(Hashtable<Integer, Vector<Point2D.Double>>, String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
pointHashtableToStringX(Hashtable<Integer, Vector<Point2D.Double>>, String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
pointHashtableToStringY(Hashtable<Integer, Vector<Point2D.Double>>, String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
pointNum - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: The number of border points.
pointOrderWasChanged(MTBPolygon2D, C2DPolygon) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper: Checks if order of points was changed during initialization.
points - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Set of border pixels.
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: List of polygon points.
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Pixels belonging to region.
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Points belonging to the region
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D: Points belonging to the region
points - Variable in class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet: Input set of points.
points - Variable in class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet: Input set of points.
pointVectorToString(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
pointVectorToStringX(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
pointVectorToStringY(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
poisson2gauss - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Flag to activate Poisson-to-Gaussian noise transform.
poisson2gauss(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Transforms image with poisson noise to image with gaussian noise J.
PoissonDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl: Poisson distribution.
PoissonDistribution(double, Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution: Constructor for Poisson distribution with parameter lambda (=mean=variance)
poll() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList: retrieve element with highest priority
polygonSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: The set of polygons represented as a Vector.
polygonSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI: Set of 2D polygons.
polys - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Result polygon set, if target format are polygons or snakes.
popUpChart() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton: Shows the chart to the user.
popUpImage(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing: Shows an image to the user.
portHashAccess - Variable in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools: Access object for port hash.
posDir - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
position - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage: Position where to draw the string.
postProcessAfterGrowing(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Here we do some morphological operations to the shape of the regions from the region growing of XylemGrower.
postprocessedImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor: Postprocessed skeleton image.
postprocessedImg - Variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor: Postprocessed skeleton image.
postProcessImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Post-process the vesselness filter result.
postprocessIndentationSegments(MorphologyAnalyzer2DInProData) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper: Post-process indentation segments to get more information on protrusions.
postprocessProtrusionSegments(MorphologyAnalyzer2DInProData) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper: Post-process protrusion segments to get more information on indentations.
potential - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Potential of the vector field.
PotentialFinderOptFunction(boolean) - Constructor for class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction: Default constructor.
potentialNewPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Phases the current pixel is (topologically) allowed to change to.
potFinder - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Helper object for reconstructing potential from vector field.
pow(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Raise image values to the power of 'constant'
pow(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Raise image values to the power of 'exponent'
ppm - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
PRA - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Check if you want to compute Pratt's figure of merit
PRA() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_PrattsFigureOfMerit: This method is the implementation of Pratt's figure of merit.
precision - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc: Precision value.
PrecisionCalc() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc: Default constructor.
PrecisionCalc(Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc: Constructor with inputs.
precursorMap - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Map of precursor positions for each pixel in the background.
predecessor - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
predecessors - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Map of precursors on contour for each pixel in narrow-band.
predict() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
predict() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetPredictionFilter: Prediction step method
predict() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
predict(LinearTransformGaussNoise) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
predictIndep(int, LinearTransformGaussNoise) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
predictors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter: dynamic models
prepareAdditionalResultDataStack(String) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
prepareFinalResultStack - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Flag for preparing final result image(s) stack.
prepareImageStack() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Puts all result images into a stack.
prepareMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Preprocess the matrix.
prepareResultImage(MTBImageShort) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D: Prepare visualization of result.
prepareResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Prepare visualization of result data by overlay on input image.
prepareResultImageStack() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Initialize result image stack.
prepareResultImageStack(Vector<MTBImage>) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Initialize result image stack.
prepareWekaData() - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans: Converts the given data set into Weka instances.
preprocess(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
preprocess(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
PreprocessLabelImages - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures: Helper class to preprocess label images for segmentation evaluation.
PreprocessLabelImages() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: Default constructor.
PreprocessLabelImages(MTBImage, MTBImage, ArrayList<Integer>, ArrayList<Integer>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: Constructor.
preprocessPlastidRegions() - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Pre-filtering of plastid regions to find regions accidentally including already a stromule.
preSegmentation() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Method for pre-segmentation.
preserveTopology - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
preserveTopology - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
prev - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
previousEnergy - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Snake energy in previous iteration (for change assessment).
previousSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Old snake of previous iteration (for evolution assessment).
prevSegment - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Reference to the preceeding segment along the contour.
print() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Print the whole MTBGraph with all its nodes and edges.
print() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Print the neurite skeleton graph informations.
print() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Prints parameters of curve to standard output.
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Print this energy object - including the value of the energy for phi assumed to be associated with this energy object.
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
print() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: Print information of this class to stdout
printData() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
printData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: Recursively prints the data contained in the nodes of the tree.
printData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData: Method to print the data associated with the node.
printData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
printData() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
printData() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
printHelp() - Static method in class cmdTools.cellAnalysis.ParticleDetector2D
printHelp(String, String) - Static method in class cmdTools.mtb_imagetools.ImageConvert
printHelp() - Static method in class cmdTools.tracking.multitarget.EvalTracks
printHelp() - Static method in class cmdTools.tracking.multitarget.ObservationSeriesGenerator
printHelp() - Static method in class cmdTools.tracking.multitarget.ObservationsInfo
printHelp() - Static method in class cmdTools.tracking.multitarget.RBMCDATracker
printHelp() - Static method in class cmdTools.visualization.DisplayImage
printMatrix(Double[][]) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
printNbPhases(short[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Print current parameter settings to standard output device.
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy: Print important parameters to standard output stream.
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Print important parameters to standard output stream.
printPoints() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Prints points of snake to standard output stream.
printReadabeTimeInfo(long) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
printTiming - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: Should time of processing be printed to stdout
printTree() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree: Prints tree data.
priority - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
prob - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
ProbabilityDensityFunction - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for multivariate distributions that allow evaluation of their probability density function.
ProbabilityMassFunction - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for univariate distributions based on probability mass functions
ProbTreeData() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
processedImage - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
processedRegionsToBinImage(MTBImage, MTBRegion2DSet, int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Create a binary image from given regions.
processImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Main image analysis routine.
processImage(MTBImage, double, double) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Convert a single image to a heatmap.
processImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Convert a single image.
processMode - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Processing mode.
ProcessMode() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess.ProcessMode
processMode - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
processMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Process mode.
profile - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile: Profile data along longest skeleton path.
profilePoints - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile: Points of the profile (neurite region) belonging to the longest path.
profileVector - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
projectAlongC - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Enables/disables projection along c-dimension.
projectAlongT - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Enables/disables projection along t-dimension.
projectAlongX - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Enables/disables projection along x-dimension.
projectAlongY - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Enables/disables projection along y-dimension.
projectAlongZ - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Enables/disables projection along z-dimension.
projector - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter: observation model
projMode - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Projection mode.
propertyChange(PropertyChangeEvent) - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane: Changes the available options of the reader option panel according to the selected files
propertyChange(PropertyChangeEvent) - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane: Changes the available options of the writer option panel according to the selected file filter of the file chooser
protrusionCounts - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
protrusionSegs - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData: List of protrusion segments along the contour.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData: Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerImageData: Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerRegion2DSet: Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerSegResultParticlesMultiChannel: Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerTableModel: Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtColorDataIOCmdline
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtPoint2dDataIOCmdline
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBImageDataIO: Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO: Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBWrapperDataIOCmdline: Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.RandomGeneratorDataIOCmdline
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing: Interface method to announce class for which IO is provided for
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing: Interface method to announce class for which IO is provided for
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing: Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBWrapperDataIOSwing: Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtColorDataIOXmlbeans
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtPoint2dDataIOXmlbeans
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBDataIOFileXmlbeans
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBImageDataIOXmlbeans: Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBTableModelDataIOXmlbeans: Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBWrapperDataIOXmlbeans: Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.RandomGeneratorDataIOXmlbeans
providedClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
providedClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing: Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOXmlbeans
providedClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing: Interface method to announce class for which IO is provided for.
providerClass - Variable in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools: Version provider class to be used in the current session.
psi - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
pstate - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter: state distribution: independent Gaussian mixtures for each target
pUpdater - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Parameter update strategy.
pUpdater - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Parameter update strategy.
putValue(int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Put a new RGB value at the specified position.
putValue(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Put a new RGB value at the specified position in the actual slice.
putValueB(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Put a new blue value at the specified position.
putValueB(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Put a new blue value at the specified position in the actual slice.
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the value of the 5D image at coordinate (x,y,z,t,c) using a Double
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the value of the current slice at coordinate (x,y,z) using a Double
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the value of the current slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Set the value of the 5D image at coordinate (x,y,z,t,c) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Set the value of the 5D image at coordinate (x,y,z,t,c) using a Double
putValueG(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Put a new green value at the specified position.
putValueG(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Put a new green value at the specified position in the actual slice.
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the value of the 5D image at coordinate (x,y,z,t,c) using an Integer
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the value of the current slice at coordinate (x,y,z) using an Integer
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the value of the current slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator: Set the value of the 5D image at coordinate (x,y,z,t,c) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Set the value of the 5D image at coordinate (x,y,z,t,c) using an Integer
putValueR(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Put a new red value at the specified position.
putValueR(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Put a new red value at the specified position in the actual slice.

Q

Q - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians: Gaussian process noise covariance matrix
qsize - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
qsize - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
quality - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
quality - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
qualpanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
quit() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Clean-up on termination.
qxy - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
qxy - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
qxy_ - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
qxy_ - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM

R

R - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians: Gaussian measurement noise covariance matrix
radiiMaxInscribedEmptyCircles - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
RadioButtonPanel - Class in de.unihalle.informatik.MiToBo.gui: A panel with a titled border and a set of radio buttons that can be reconfigured easily.
RadioButtonPanel(String) - Constructor for class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel: Constructor
radius - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Radius of the node
radius - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
radius - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Neighborhood radius for LBP code calculation.
radiusImg - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Optional radius image.
radiusScale - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPsRIU: Scale factor for radius.
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution: random generator for sampling
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
rand - Variable in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution: random generator for sampling
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
rand - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
random - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Random generator for color sampling.
randomColor(Random) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Generates the next random color.
RandomGeneratorChooser(Random, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
RandomGeneratorDataIOCmdline - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline: Data I/O provider for ALDOpRunner (commandline) for java.util.Random objects.
RandomGeneratorDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.RandomGeneratorDataIOCmdline
RandomGeneratorDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing: Data I/O provider for GUI-OpRunner for java.util.Random objects.
RandomGeneratorDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing
RandomGeneratorDataIOSwing.RandomGeneratorChooser - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
RandomGeneratorDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans: Xmlbeans provider forjava.util.Random objects.
RandomGeneratorDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.RandomGeneratorDataIOXmlbeans
randomSeed - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
randomSeed - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
RangeColor() - Constructor for enum de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage.RangeColor
rangeMax - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Maximum value of mapping range, will be mapped to second color.
rangeMin - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Minimum value of mapping range, will be mapped to first color.
rankedValueAt(int, int, int, int, int, MTBImage, double[]) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Compute rank operator value for coordinate (x,y,z,t,c) Treatment at boundaries: Image values are mirrored at the border element to determine values under the mask that are outside the image.
rankOp(MTBImage, RankOperator.RankOpMode, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Compute the rank operation of a gray-valued image, stack or hyperstack
RankOperator - Class in de.unihalle.informatik.MiToBo.filters.nonlinear: Rank operator class to compute Median, Minimum or Maximum filter for hyperstack, stack and plain images.
RankOperator() - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Constructor
RankOperator(MTBImage, RankOperator.RankOpMode, int) - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Constructor
RankOperator(MTBImage, RankOperator.RankOpMode, int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Constructor
RankOperator.RankOpMode - Enum in de.unihalle.informatik.MiToBo.filters.nonlinear: Defines the operation
rankOpMode - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
RankOpMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator.RankOpMode
rbbox - Variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel: vertical box to place the radio buttons on the panel
rbgroup - Variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel: the logical group of radio buttons
RBMCDASample<T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl: Representation of a RBMCDA-sample.
RBMCDASample() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample: Constructor.
RBMCDASample(MultiTargetPredictionFilterIndep<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample: Constructor with an initial prediction filter.
RBMCDASampleInfo<T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl: RBMCDA-sample info object.
RBMCDASampleInfo() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
RBMCDASampleInfo(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
RBMCDASampleInfo(RBMCDASampleInfo<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
RBMCDATracker - Class in cmdTools.tracking.multitarget: Commandline tool for multi-target tracking with RBMCDA-framework described in [Gress,Posch, "
RBMCDATracker() - Constructor for class cmdTools.tracking.multitarget.RBMCDATracker
read(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Read a contour set from an xml file filename and set the MTB polygon set accordingly.
read(MTBXMLContour2DSetType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Read a contour set from an xml object xmlContourSet and set the MTB polygon set accordingly.
read(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Read a polygon set from an xml file filename and set the MTB polygon set accordingly.
read(MTBXMLPolygon2DSetType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Read a polygon set from an xml object xmlPolygon2DSet and set the MTB polygon set accordingly.
readBorderFromASCIIFile(String, String, int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Read a 2D border object from an ASCII file in xSV format.
readBordersFromASCIIFiles(String, String, int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Read a set of 2D border objects from ASCII files in xSV format from the given directory.
readContourFromASCIIFile(String, String, int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Read a 2D contour object from an ASCII file in xSV format.
readContoursFromASCIIFiles(String, String, int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Read a set of 2D contours from ASCII files in xSV format from the given directory.
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel: Returns the contents of the text field.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
readData(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile
readData(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBImageDataIO
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
readData() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel: Gets the current coordinates.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage: Function to get selected image from GUI.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBWrapperDataIOSwing
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtColorDataIOXmlbeans
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtPoint2dDataIOXmlbeans
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBDataIOFileXmlbeans
readData(Field, Class<?>, ALDXMLObjectType) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBImageDataIOXmlbeans
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBTableModelDataIOXmlbeans
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBWrapperDataIOXmlbeans
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.RandomGeneratorDataIOXmlbeans
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton: Gets the data from the configuration window.
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Extracts current collection data.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOXmlbeans
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton: Gets the data from the configuration window.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Extracts current data.
reader - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
READER_OPTIONS_APPROVED_PROPERTY - Static variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane: Property change when writer options are approved (i.e. when filechooser selection is approved)
readFromBinFile(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Reads a vector field from a file in binary format.
readImage(String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
readImagePlus(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Read image imageIdx from the specified file and return it as ImagePlus object.
readImgProperties(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
readInputImageMaxProjectChannel(String) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Read image from file, do optional max projection and extract selected cytoskeleton channel.
readMarker(NodeList, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
readMarkerData() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
readMaskImage(String, double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Read mask data from disk if available.
readMaskImage(String, String, CytoskeletonFeatureExtractor.CellMaskFormat, double, double, double, double, boolean) - Static method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Read mask data from disk if available.
readMTBImage(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Read image imageIdx from the specified file and return it as MTBImage object.
readMultiStates(String) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.MultiStateIO: Read a vector of MultiState objects from a file with xml-beans representation.
readResolve() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperator: Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
readResolve() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage: Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Function for proper initialization of deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Function for proper initialization of deserialized objects.
readSingleValue(Document, String) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
readValue(NodeList, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
ReadXML - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml: Reads markers of an image from file in XML format.
ReadXML(String) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML: Creates a new instance of ODReadXMLODD
recalcHueMean(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D: Recalculate the mean including incrementing the number of pixels with define hue value, i.e. the number of pixels contributing to the hue sum.
recalcSatMean(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D: Recalculate the saturation of the region including incrementing the number of pixels with define saturation value, i.e. the number of pixels contributing to the saturation sum.
recalcXMean(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D: Recalculate the X(Intensity / Brightness / Value )-value of the region.
recall - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc: Recall value.
RecallCalc() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc: Default constructor.
RecallCalc(Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc: Constructor with inputs.
recursiveBox - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel: Flag to enable/disable recursive directory processing.
recursiveProcessing() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel: Query flag for recursive processing.
recursiveProcessing - Variable in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree: Flag for recursive processing of sub-directories.
red - Static variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Definition of red color.
RED_COMPONENT_INDEX - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
reduce() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Method which implements the dimension reduction.
ReducerMethod() - Constructor for enum de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.ReducerMethod
ReductionMode() - Constructor for enum de.unihalle.informatik.MiToBo.math.statistics.PCA.ReductionMode
refIndex - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
reflect() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement: reflects the structuring element around its center
Region2DSetFromLabelimage - Class in de.unihalle.informatik.MiToBo.segmentation.regions.convert: Operator to convert 2D label image to a MTBRegionsSet2D.
Region2DSetFromLabelimage() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage: Default constructor.
Region2DSkeletonAnalyzer - Class in de.unihalle.informatik.MiToBo.features.regions: Operator to analyze skeletons of a given set of regions.
Region2DSkeletonAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Default constructor.
Region2DSkeletonAnalyzer.FeatureNames - Enum in de.unihalle.informatik.MiToBo.features.regions: Set of region features calculated from region skeletons.
regionBinaryMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
RegionConverter(MTBRegion2D) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter: Default constructor.
regionID - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
regionID - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Region ID of the corresponding neurite region to this neurite skeleton graph.
RegionImageConverter(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter: Default constructor with parameters.
regionIO - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to read a region set.
regionIObin - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to configure binary mode for region sets.
regionMeans - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: List of calculated region average values.
regions - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Result region set, if target format are regions.
regions - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
regions - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
RegionSelector() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
RegionSelector(MTBRegion2DSet, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
regionSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: The set of regions represented as a Vector.
regionSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: The set of regions represented as a Vector.
regionSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI: Set of 2D regions.
regionSet - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
regionSet - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage: Resulting region set.
regionsets - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag: the container of the region sets
regionSizes - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: List of calculated region sizes.
regionsToBinImage(MTBImage, MTBImage, Vector<MTBRegion2D>) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Create binary image from a set of regions.
regionsToObservations(boolean, MTBRegion2DSetBag) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter: Convert regions to observations
regionToFile(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Write the coordinates of the included 3D points into a text file.
regionTouchesBoundary(MTBRegion2D, int, int) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Test whether a region is located at, i.e. touches, the boundary of the image.
regionVars - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: List of calculated region variance values.
regionVoronoize() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Function to perform Voronoi tesselation.
register(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess: Registers the object to the database.
registerImageBox(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess: Registers the given (image) object.
reinitOperator() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Re-initialize the operator just in case it was already run before.
relabel(byte[][], int, int, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite: find and assign object labels to segmented objects in two frames
relabelRegion(MTBImageByte, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Set the unique id of the given region to the pixel value found at the coordinate of the first pixel in the region on the pre labeled MTBImageByte.
relTo(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
remove() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
remove(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
remove() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
remove(MTBLineSegment2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: Delete the given lineobject from the set, if contained.
remove(Point2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
remove(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
remove(MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Delete the given region object from the set, if contained.
remove(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag: Remove a region set from this bag
remove(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag: Remove a region set from this bag by its index
remove() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIterator
remove() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelIndexIterator
remove() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
removeBorderObjects - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
removeBorderObjects - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
removeChild(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: Remove child node.
removeEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Remove the specified edge from the graph
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Delete the i-th border from the set.
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Delete the i-th contour from the set
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: Delete the i-th segment from the set.
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Delete the i-th region from the set
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Delete the i-th region from the set
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Delete the i-th region from the set
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Removes the element at the specified position in this list.
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet: Removes the element at the specified position in this list.
removeEnergyButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Remove button for energies.
removeExcluded - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
removeExcluded - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
removeExcludedObjects(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
removeExtension(String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator: Remove extension from filename if any.
removeFirst() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Removes and returns the first element from this list.
removeImage(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
removeIndepGaussian(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians: Remove independent Gaussian state distribution (at index i)
removeInEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Remove a incoming MTBGraphEdge from the MTBGraphNode.
removeItem(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult: Remove an item from the set.
removeItem(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves: Remove an item from the set.
removeItem(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Remove an item from the set.
removeLast() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Removes and returns the last element from this list.
removeLastItem() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult: Removes the last data item.
removeLastItem() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves: Removes the last data item.
removeLastItem() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions: Removes the last data item.
removeLastMarker() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Removes the last marker from the vector.
removeLeadingDirectories(String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator: Remove all leading pathname components from a filename.
removeMarker(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Deletes marker with given index from vector.
removeNode(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph: Remove the specified node from the graph as well as the edges connected to it.
removeOutEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode: Remove a outgoing MTBGraphEdge from the MTBGraphNode.
removeShortRuns(int[], int, int) - Static method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper: Function to remove all sub-sequences of target shorter than the given minimum length by replacing them with negated target.
removeSmallComponents(MTBImageByte, int) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Remove small componentes from an image of type MTBImageByte.
removeSpines - Variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor: Flag to enable/disable spine removal.
removeState(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState: Remove the idx-th state (indices start from 0)
removeState(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
rEngine - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: JRI R engine to run R as a single thread.
rEngine - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: R engine to start R thread.
rEngine - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: R engine to call R scripts.
rEngine - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: JRI R engine to run R as a single thread.
replacementPattern - Variable in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
replacementString - Variable in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
report - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
report - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
ReportGenerator - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
ReportGenerator() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
requiresCounterClockwiseContourSorting() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable: Ask energy if contour points need to sorted counter-clockwise.
requiresCounterClockwiseContourSorting() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCoupled: Ask energy if contour points need to sorted counter-clockwise.
requiresCounterClockwiseContourSorting() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable: Ask energy if contour points need to sorted counter-clockwise.
requiresNewlines() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
requiresOverlapMask() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable: Ask energy if an overlap mask for all snakes jointly optimized is required.
requiresOverlapMask() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCoupled: Ask energy if an overlap mask for all snakes jointly optimized is required.
requiresOverlapMask() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable: Ask energy if an overlap mask for all snakes jointly optimized is required.
res_x - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
res_y - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
resample(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Method to re-sample the line segments of the polygon in a range of a given segment length.
resample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Resample this distribution and equalize weights
resample(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Method to re-sample the line segments of the snake in a range of a given segment length.
resampleConstant - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
resampleConstant - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Constant for resampling the snake control points.
resampleSegLength - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Target length of snake segments in resampling.
resampleSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Resamples the snake using the specified segment length.
reset() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime: Reset time
reset() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
resetButton - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: Button to reset color to null.
resetLabel(int, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
resetPotential() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Resets the potential, next access to it will enforce recalculation.
resetShape() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Delete shape object, i.e. reset to null.
resizeMatrices() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Resize parameter matrices.
ResponseDifference(double, double) - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.ResponseDifference: Default constructor.
responseStack - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Stack with filter responses of all orientations.
responseStack - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D: Result stack with binary vessel maps for different scales and lengths.
responseStack - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Result stack with intermediate results.
restoreConfigWins() - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab
result - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
result_energy - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Result directory for snake energy results.
result_extraction - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Result directory for neurite extraction results.
result_presegmentation - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Result directory for pre-segmentation.
result_snakes - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Result directory for snake results.
resultAdditionalImages - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Additional result images condensed into a single stack (only available if PaCeQuant.showAdditionalResultImages is true).
resultAreas - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
resultBinaryImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult: Binary image with segmented regions in foreground (white).
resultBinFilteredImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Filtered binary vesselness image.
resultBinVesselImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Binarized vesselness image.
resultBorders - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Set of extracted borders.
resultCellContours - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: ROI set of detected cell regions.
resultCellImg - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Input image with snake contours overlayed (optional).
resultCellLabelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Label image of detected cell regions.
resultCellLabelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Label image of detected cell regions.
resultCellOverlayImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Overlay of input image with pseudo-colored cell regions.
resultCellRegions - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Set of detected cell regions.
resultCenters - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Set of detected nuclei centers.
resultContourImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
resultContours - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: * The calculated contours, every contour can include several inner contours.
resultCosts - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Costs of the result path.
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Result data object.
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Result data object.
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Result data object containing quantitative data and label images.
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Vector of result data objects.
resultData - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Result of the calculation.
resultData - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Resulting data set with each column containing a data vector.
resultDataAreaFractions - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Result data: area fractions.
resultDataAvgSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Result data: average size.
resultDataCells - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Local container for cell cytoplasm segmentation result.
resultDataCellSizes - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Result data: cell sizes.
resultDataCounts - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Result data: counts.
resultDataTotalSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Result data: total structure size per cell.
resultDir - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Main directory for result output.
resultDisplayMode - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D: Mode of how to display result image.
resultDisplayMode - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Mode of how to display result image.
resultFeatureStack - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Stack of individual feature images as heat maps (only available if PaCeQuant.showResultFeatureStack is true).
resultFeatureTable - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Table with region features.
resultFeatureTable - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Table with region skeleton features.
resultFile - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Optional file where to save the result table.
resultImage - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Result segmentation image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
resultImage - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Optional stack of result visualizations, if result data suppports that.
resultImage - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Several result formats.
resultImage - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression: Resulting thinned (and thresholded) magnitude image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Output image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Image of extracted borders.
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: * The binary image with the calculated contours and the contours as possible outputs from the operator.
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding: Resulting binarized image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
resultImage - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
resultImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet: Result image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet: Result image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Output image.
ResultImageMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D.ResultImageMode
ResultImageMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D.ResultImageMode
resultImagePlus - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
resultImages - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Local container for set of segmentation result and channel copy images.
resultImages - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Vector for collecting result images.
resultImageStack - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: (Optional) stack of result images with segmentation masks/overlays.
resultImageType - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
resultImageType - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
resultImageType - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D: Result label image of separated nuclei.
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos: Result label image of separated nuclei.
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Stack with result overlays corresponding to channels.
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
resultImg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
resultImg - Variable in class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching: Result image with stretched contrast.
resultImg - Variable in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization: Result image with improved contrast.
resultImg - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Enhanced or segmented result image, either of type double or binary.
resultImg - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D: Filtered image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
resultImg - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Result image with path overlay, start pixel in green, end pixel in blue.
resultImg - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgClose
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgErode
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor: Binary result image, skeleton in white, background in black.
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.WatershedBinary: Segmented binary image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours: Result image showing the ground truth image and the segmented contours.
resultImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
resultImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: Result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter: Result image displaying the snakes as overlay.
resultImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
resultImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer: Result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
resultImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Result image (stack).
resultImg - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: Generated result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Generated result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Generated result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D: Result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage: Result image.
resultImgHeight - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Desired height of result image.
resultImgIntermediate - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Debug image with intermediate result data.
resultImgOffsetX - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Desired offset in x of result image.
resultImgOffsetY - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Desired offset in y of result image.
resultImgWidth - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Desired width of result image.
resultInfo - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Info string for segmentation phase configuration parameters.
resultingRegions - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Set of detected particle regions.
resultingRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Resulting set of labeled regions.
resultingRegionsets - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
resultInitialSkeletonImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Initial skeleton image.
resultJunctions - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Detected junction points.
resultLabelImage - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT: Label image of detected plastid regions with stromuli.
resultLabelImage - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Label image of detected plastid regions with stromuli.
resultLabelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult: Result image with labels of segmented regions.
resultLableImgWithoutIDs - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult: Label image without region ID strings.
resultLines - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Detected lines.
resultList - Variable in class de.unihalle.informatik.MiToBo.color.tools.DistinctColorListGenerator: Color list.
resultLobeFeatureTables - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: (Optional) set of tables with type information and features per lobe.
resultLobeTypeImage - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Image showing lobe classification.
resultMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
resultMaskBinary - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Binary mask of detected regions.
resultMatrix - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite: Result matrix containing final matching.
resultMaxRegionSizeThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Used threshold for maximal size of valid regions.
resultMinRegionSizeThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Used threshold for minimal size of valid regions.
resultMSERs - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Set of detected MSER regions.
resultMTBImage - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
resultMTBImg - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Result Image.
resultObj - Variable in class de.unihalle.informatik.MiToBo.features.FeatureCalculator: Result data object, e.g., an image, a histogram, a vector, ....
resultOverlay - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Detected regions plotted into input image.
resultOverlayImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult: Image overlay of detected regions over input image.
resultOverlayImgWithoutIDs - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult: Image overlay of detected regions over input image without ID strings.
resultPath - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Result path represented as point list.
resultRegCenters - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Nuclei centers sorted according to former regions.
resultRegionCount - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Number of detected regions.
resultRegs - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult: Set of segmented regions.
resultRGBimage - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: RGB image overlay with result nuclei contours.
resultSet - Variable in class de.unihalle.informatik.MiToBo.io.importer.GetMTBContour2DSetFromXSVFiles: Resulting contour set.
resultSkelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Skeleton image (of cell boundaries).
resultSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
resultsTable - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
resultsTable - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
resultsTable - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
resultsTable - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: A table containing information for each region
resultsTable - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: A table containing information for each region
resultStats - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Result data object.
resultTable - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Result table showing the the detection and morphology measurements.
resultTable - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
resultTable - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult: Result table for visual result inspection.
resultTable - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Table with result data.
resultTreelines - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Resulting enhanced treeline annotations.
resultType - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Type of result features to be returned.
resultType - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Desired type of result.
ResultType() - Constructor for enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.ResultType
resultValue - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
resultValueMode - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer: Result value mode.
ResultValueMode() - Constructor for enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.ResultValueMode
resultVector - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel: Name of the analyzed image.
resultVesselImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Result of applying the vesselness filter to the input image.
resultVesselMap - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Final vessel map.
resultVesselMap - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D: Resulting binary vessel map.
resultVesselMap - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Resulting binary vessel map.
resultXylemRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: Final xylem regions after postprocessing.
resultXylemRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Final xylem regions after post processing.
reversePolypoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Changes the ordering of the polygon points.
reversePolypoints() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Overwrite reversePolypoints method of Polygon2D.
revisionFile - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile: Name of revision file from where to read revision information.
rgbColor - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter: Resulting RGB values.
rgbColor - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter: Resulting RGB values.
rgbOutput - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter: Output RGB values.
rgbToHSB_JRE(int[]) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Conversion from RGB into HSB color space.
rgbToHSI_Sonka(int[]) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Conversion from RGB to HSI color space according to Sonka et al.
rgbToHSV_EasyRGB(int[]) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Conversion from RGB into HSV color space.
RGBToHSXConverter - Class in de.unihalle.informatik.MiToBo.color.conversion: Converts an image of type MTBImageRGB ( RGB color space ) into an image with HSX( hue saturation intensity/brightness/value ) color space.
RGBToHSXConverter() - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Default constructor.
RGBToHSXConverter(MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Constructor.
RGBToHSXConverter.ColorChannel - Enum in de.unihalle.informatik.MiToBo.color.conversion: Supported Color Channels.
RGBToHSXConverter.Mode - Enum in de.unihalle.informatik.MiToBo.color.conversion: The way of converting an image from rgb to hsi.
rgbValue - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
rho - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Weighting factor and overlap penalty, respectively.
rightBorderPoint - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Right boundary point of segment after potential shifts.
rightBorderPointPosOnContour - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Index of right boundary point of segment after potential shifts.
rightOutlierFraction - Variable in class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching: Fraction of outlier pixels at right histogram margin.
roiAdapt - Static variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: The object instance.
roiFile - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter: Input ROI file or zip archive with ROIs.
RoiFileToCSVConverter - Class in de.unihalle.informatik.MiToBo.core.imageJ: Operator to convert contours of ImageJ ROIs to CSV format.
RoiFileToCSVConverter() - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter: Default constructor.
roiManager - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Reference to the current ImageJ roi manager.
RoiManagerAdapter - Class in de.unihalle.informatik.MiToBo.core.imageJ: Convenience functions for interaction with ImageJ's ROI manager.
RoiManagerAdapter() - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter: Hidden constructor, never called from outside.
RoiManagerAdapter.RoiReader - Class in de.unihalle.informatik.MiToBo.core.imageJ: Class for parsing ImageJ roi files and zip archives.
RoiManagerAdapter.RoiReader.TargetFormat - Enum in de.unihalle.informatik.MiToBo.core.imageJ: Format into which the ROIs should be converted.
roiManagerAdd - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
roiManagerChecker - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
RoiReader(String, RoiManagerAdapter.RoiReader.TargetFormat) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Default constructor.
roisAdded - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
roisAdded - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
roisAdded - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
roitable - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Helper hash table.
RoiWriter - Class in de.unihalle.informatik.MiToBo.core.imageJ: Operator to save data objects to native ImageJ ROIs.
RoiWriter() - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter: Default constructor.
root - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree: Root node of the tree.
RootImageSegmentationOperator - Class in de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation: Abstract super class for operators segmenting roots from images.
RootImageSegmentationOperator() - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Default constructor.
RootImageSegmentationOperator.LayerSubset - Enum in de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation
RootImageSegmentationOperator.OpWorkingMode - Enum in de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation
ROOTSEGMENT_STATUS() - Constructor for enum de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing.ROOTSEGMENT_STATUS
rotatePoint2D(Point2D.Double, double) - Static method in class de.unihalle.informatik.MiToBo.math.MathXGeom: Rotate a 2D point around the given angle.
rotatePoint2D(double, double, double) - Static method in class de.unihalle.informatik.MiToBo.math.MathXGeom: Rotate a 2D point around the given angle.
roundnessThreshold - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Roundness threshold for components.
rowMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Array containing row marks.
rows - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Number of rows of the table.
rsize - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
rsize - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
run() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D.UWTRunner
run() - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane.FileOptionsRefresher
runFeatureExtractionPhase(MTBImage, MTBRegion2DSet, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Extracts features from given set of regions and corresponding images
runIterativeMode() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Cell tissue segmentation in an iterative fashion.
runMeanVarMode() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Deprecated.
runOperation(MTBOperator, ImageArithmetics.ArithOp, MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Run an operation with one input image and one input constant
runOperation(MTBOperator, ImageArithmetics.ArithOp, MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Run an operation with two input images
runSegmentationPhase(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Method that processes a single image.
runtime - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
runtimes - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
rxy - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
rxy - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM

S

s - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter: Array of saturation values.
s - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter: Saturation of HSV space.
s - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBStringData: The string data to store.
sampleCount - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Number of data samples in input data.
sampleEnergyData - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
sampleInfo - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
sampleinfo - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample: Properties represented by this sample.
sampleJointProb - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
SamplingDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for densities from which samples can be drawn.
satMean - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
satMTBImg - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Saturation channel image.
satSum - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
satThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: The saturation threshold.
satThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: The saturation threshold.
SATURATION_COMPONENT_INDEX - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
SATURATION_UNDEFINED - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: To cope with undefined saturation/hue-values, we use the following scheme.
save(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: write the histogram data into a text file
saveExtEnergy(String) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D: Save the gvf field in a MATLAB like file.
saveFile() - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Saves the current processing result.
saveIntermediateResultPath - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Path where to save intermediate results.
saveIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Flag for saving intermediate results to a specified directory.
saveIntermediateResults(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Set flag to save intermediate results.
saveIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Flag for saving intermediate results.
saveIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Flag to enable/disable saving of intermediate results.
saveIntermediateResultsPath - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Path where to save intermediate results.
saveIntermediateResultsPath - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Path to where intermediate results should be stored.
saveNeuriteWidthList(Vector<Double[]>, String) - Static method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Method to save the neurites width profile in a file.
savePolygon(PolygonRoi) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter: Saves the given polygon to the specified output file.
savePolygonSet(PolygonRoi[]) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter: Saves the set of polygons to the specified output file.
saveProfileSet(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Saves the given profile data list with N profiles to the given file.
saveRegionData(String, String, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Save region set to output file.
saveSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Save intermediate results.
saveSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
saveSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Save intermediate results.
saveSnakeLoc - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Path where to save intermediate results.
saveSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Flag to enable/disable saving of intermediate snake results.
saveSVM() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer: save resulting svm model file
saveTable(File) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Saves the contents of the table to given file, TSV format.
saveTilesToFiles(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Saves all tiles to the given path.
saveToBinFile(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Saves the vector field to a file in binary format.
SCALEBARWIDTH - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
scaleDown - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE: Scaling factor for normalization Still experimental
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Scale factor of the snake for normalization.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Scaling factor to rescale image coordinates in range [0,1] or several ranges to the original coordinates range like [1000, 1000] in a image of size 1000 x 1000.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Scaling factor for image coordinates.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Scaling factor for image coordinates.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Scaling factor to rescale image coordinates in range [0,1] or several ranges to the original coordinates range like [1000, 1000] in a image of size 1000 x 1000.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Scaling factor to rescale image coordinates in range [0,1] or several ranges to the original coordinates range like [1000, 1000] in a image of size 1000 x 1000.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Scale factor for snake normalization.
scaleIntervalSize - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Size of scale interval for calculating wavelet correlation images.
scaleIntervalSize - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT: Size of scale interval for calculating wavelet correlation images.
scaleMax - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
scaleMin - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
scaleNormalizationFactor - Static variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Factor to normalize filter responses of different scales appropriately.
scaleNum - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
scaleValues(int, int, double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Method to scale the intensity values (range [curMin, curMax]) of the image to a given range [scaleMin, scaleMax].
scaleValues - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
scalingK - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Niblack scaling parameter k.
scalprod(MTBLineSegment2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D: Calculates the scalar product of the given segment to this one.
scanPath - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Local flag to indicate if we are currently tracing a path for a new piece of boundary.
schwelle - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Threshold to suppress peak analysis close to scraggy contours.
ScoreInterpretation() - Constructor for enum de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm.ScoreInterpretation
scoreMatrix - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite: Matrix containing pairwise scores of bipartite sets.
scoreMatrix - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Score matrix with pairwise overlaps.
scoreMatrix - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Score matrix with pairwise overlaps.
scratchArea - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
scratchAreas - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
ScratchAssayAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.scratchAssay: class for analyzing the scratch areas in a scratch assay/ gap closure/ wound closure assay
ScratchAssayAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
ScratchAssayAnalyzer(MTBImage, int, int, ScratchAssayAnalyzer.ScratchOrientation, boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
ScratchAssayAnalyzer.AbsenceDetectionMethod - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
ScratchAssayAnalyzer.ScratchOrientation - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
ScratchAssaySegmenter - Class in de.unihalle.informatik.MiToBo.apps.scratchAssay: class for segmenting the wound area of a scratch assay image

First the image is smoothed.
ScratchAssaySegmenter() - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
ScratchAssaySegmenter(MTBImage, int, int, boolean, boolean, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
ScratchAssaySVMTrainer - Class in de.unihalle.informatik.MiToBo.apps.scratchAssay: class for training and cross validating a support vector machine for classification of scratch assay
images into images containing a scratch and those that don't
ScratchAssaySVMTrainer() - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
ScratchAssaySVMTrainer(String, String, int, int, boolean, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
ScratchAssaySVMTrainer.KERNEL_TYPE - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
ScratchAssaySVMTrainer.ScratchOrientation - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
ScratchAssaySVMTrainer.ValidationMethod - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
scratchFeatures - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
scratchFiles - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
ScratchOrientation() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.ScratchOrientation
ScratchOrientation() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ScratchOrientation
SecondOrderCentralMoment<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces: Interface for classes that provide a second order central moment.
seedImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
seedRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: The seed regions as a binary image after the final erosion.
seedRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: The seed regions as a binary image after the final erosion.
seen - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
seErosionSize - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: Size of the structuring element for the erosion.
segContours - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours: List of point-wise segmented contours.
segContours - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: List of contours of segmented objects.
segDim - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
segImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: Label image of segmentation result.
segLabelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Preprocessed segmentation label image with short pixel type.
segLabelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Label image of segmentation result.
segLabels - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages: List of labels of segmented regions.
segLabelsOrig - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Label image of segmentation result.
segLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Length of segment measured as number of pixels.
segment(MTBImage, String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
segment(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter: segment cells in a single frame of the input image
segment(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
segmentation - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Segmentation object.
SegmentationConfigWin(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Default constructor.
SegmentationDimension() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface.SegmentationDimension
SegmentationDimension() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.SegmentationDimension
SegmentationInitializer - Class in de.unihalle.informatik.MiToBo.segmentation.basics: Operator for initializing objects of type MTBSegmentationInterface.
SegmentationInitializer() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Default constructor.
SegmentationInitializer.InputMode - Enum in de.unihalle.informatik.MiToBo.segmentation.basics: Available data sources.
SegmentationInitializer.SegmentationDimension - Enum in de.unihalle.informatik.MiToBo.segmentation.basics: Available dimensions for segmentations.
SegmentationInitializer.ShapeType - Enum in de.unihalle.informatik.MiToBo.segmentation.basics: Available shape types.
SegmentationInitializerDataIOSwing - Class in de.unihalle.informatik.MiToBo.segmentation.basics: Class for loading/saving objects of type SegmentationInitializer.
SegmentationInitializerDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
SegmentationInitializerDataIOSwing.ConfigureSegmentationButton - Class in de.unihalle.informatik.MiToBo.segmentation.basics: GUI element for configuring segmentations.
SegmentationInitializerDataIOSwing.SegmentationConfigWin - Class in de.unihalle.informatik.MiToBo.segmentation.basics: Segmentation configuration window.
segmentationInputFormat - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Format of external segmentation input.
SegmentationInputFormat() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationInputFormat
SegmentationMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete.SegmentationMode
segmentationParameters - Static variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: List of parameters relevant for segmentation phase.
SegmentationResult() - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult
segmentationResult - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
segmentInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Preprocessing and segmentation of input image.
segmentlength - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Snake segment length.
SegmentType() - Constructor for enum de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.SegmentType
segMode - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Mode how the channel of the image was treated during segmentation.
segObject - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
segRegionLabels - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours: List of labels of segmented regions.
SegResult_Complete - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages: Complete segmentation result from multi-channel image.
SegResult_Complete(String, int, SegResult_Complete.SegmentationMode, SegResult_Cytoplasm) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Default constructor.
SegResult_Complete.SegmentationMode - Enum in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages: Indicator for segmentation mode.
SegResult_Cytoplasm - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages: Cell boundary segmentation result from single-layer image.
SegResult_Cytoplasm(String, MTBPolygon2DSet, MTBImageByte, int, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Deprecated.
SegResult_Cytoplasm(String, MTBPolygon2DSet, MTBImageByte, int, int[], double) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Default constructor.
SegResult_Interface - Interface in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages: Interface for unified handling of segmentation results extracted by particle, cell or nucleus detectors.
SegResult_Nuclei - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages: Nuclei segmentation result from a single image channel.
SegResult_Nuclei(String, int, MTBImageByte, MTBImage, MTBRegion2DSet, int, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Default constructor.
SegResult_Particles - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages: Particle detection result for a single channel of an image.
SegResult_Particles(String, int, MTBRegion2DSet, MTBImageByte, int, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Default constructor.
SegResult_ParticlesMultiChannel - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages: Particle detection result for a multi-channel image.
SegResult_ParticlesMultiChannel(String) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel: Default constructor.
SegResultEnums - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages: Defines of enumeration types used in conjunction with cell image analysis.
SegResultEnums() - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResultEnums
SegResultEnums.MeasureUnit - Enum in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages: Unit for measurements.
selectBox - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage: Combobox to select images.
selectButton - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: Button to open selection window.
selectedEnergies - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: List of currently selected energies.
selectedEnergies - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: List of currently selected energies.
selectedImage - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage: Recently selected image.
selectFileDir - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel: Button to select via dialogue.
selection - Variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel: string/label of the selected radio button
SELECTION_CHANGED_PROPERTY - Static variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel: Property change of the panel when a selection is changed
selectLargeRegions(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
semiAxisLengthA - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Half-length of axis a.
semiAxisLengthB - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D: Half-length of axis b.
seOpeningSize - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: Size of the structuring element for Opening.
seOpeningSizeInitSeg - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: Size of the structuring element for Opening.
separate(int, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: try to separate component with label 2.
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel
serialVersionUID - Static variable in exception de.unihalle.informatik.MiToBo.io.images.OverwriteException
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel: Default serial number.
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow.MTBSet_SnkEnergyPDEGUITableModel: Default serial number.
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
seriesIndices - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
seriesnames - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
seriespanels - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
set(int, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
set(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: assign a value to the matrix at position ( x, y, z )
setActive() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Set marker active.
setActivityArray(boolean[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Specify set of active snakes.
setActualSliceOnly() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Only actual slice is thresholded, this will force the output image type to be of the same type as the input image (or destination image type)
setAdjacencyMatrix(AdjacencyMatrix<T>) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter: Set the main graph's adjacency matrix
setAlgorithm(Contour2DCurvatureCalculator.Algorithm) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
setAnalyzeProtrusionsAndIndentations(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Turn on/off analysis of contour protrusions and indentations.
setAngle(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D: Set orientation of filter.
setAngleSampling(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Set angular sampling interval.
setArithmeticOperation(ImageArithmetics.ArithOp) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
setAssociation(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
setAssociation(int, int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation: Set an association between target and observation.
setAvgIntensity(double) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape: Set average region intensity.
setBaselineConstant(double) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Specify baseline constant for thresholding.
setBGOriginalValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Tell the thresholder to use the original pixel value for background pixels
setBGValue(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Set value of Parameter argument BGValue.
setBinaryImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set the binary image.
setBinValue(int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: set the bin value at i-th position
setBorderExclusion(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing: should border touching objects be excluded
setBorderType(BordersOnLabeledComponents.BorderType) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Set border type to be extracted.
setBoundaryPadding(MTBImageWindow.BoundaryPadding) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Set value of Parameter argument boundaryPadding.
setBoundaryPadding(MTBImageWindow.BoundaryPadding) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Set value of Parameter argument boundaryPadding.
setBoundaryPadding(MTBImageWindow.BoundaryPadding) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Set value of Parameter argument boundaryPadding.
setBthMaskSize(Integer) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Set mask size of black top-hat.
setC(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setCalcArea(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
setCalcCircularity(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Turn of/off calculation of circularity.
setCalcCompactness(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
setCalcConcavityData(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Turn on/off calculation of concavity information.
setCalcConvexHullMeasures(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Turn on/off calculation of convex hull measures.
setCalcEccentricity(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Turn of/off calculation of eccentricity.
setCalcLengthWidth(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Turn of/off calculation of region length and width.
setCalcMarginRoughness(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Turn on/off calculation of margin roughness values.
setCalcPerimeter(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
setCalcSkeletonBranchFeatures(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Turn on/off calculation of skeleton branch features.
setCalcSolidity(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Turn on/off calculation of solidities.
setCalcSurfArea(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
setCalcVolume(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
setCalibration(Calibration) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the calibration object (see getCalibration() for further information).
setCalibrationFromUnderlyingIJImage() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the MiToBo image calibration reference to underlying ImagePlus calibration.
setCategoryColors(Color[]) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Specify colors for different categories.
setCategoryColors(Color[]) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Specify colors for different categories.
setChannel(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
setChannel(Integer) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Set the image channel.
setChannelsAreRGBFlag(Boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter: Set flag if RGB color channels are interpreted as real image channels.
setChannelsToCopy(int[]) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Specify list of channels to copy to result stack.
setChosenColor(Color) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: Select given color.
setClass(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
setClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
setClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
setClass(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
setClass(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Set the label of position (x,y) to c.
setClass(int, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Set the label of position (x,y,z) to c.
setClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Deprecated.
setClass(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Deprecated.
setClass(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Deprecated.
setClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Deprecated.
setCloneTargetImage(boolean) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Enable or disable cloning of target image.
setClosed() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Set polygon closed.
setClusterNum(int) - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans: Specify number of clusters.
setCodec(Integer) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Set the codec (quicktime only).
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Set color of markers.
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet: Specify color in which to draw the contours.
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Specify color to use.
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine: Specify color to use for drawing.
setColor(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D: Specify color as integer value, right 24 bits are interpreted as R,G,B.
setColor(String) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet: Specify color in which to draw the snakes.
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Set the uniform color of the regions in a color image.
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage: Specify color.
setColor(int, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT: Set the color for given key.
setColorArray(int[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Specify pseudo-colors for snake visualization.
setColorImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Add the label image to the parameter object
setColorNumber(int) - Method in class de.unihalle.informatik.MiToBo.color.tools.DistinctColorListGenerator: Set number of colors.
setColorRangeMaximum(Color) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper: Color for range maximum.
setColorRangeMaximum(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Color for range maximum.
setColorRangeMinimum(Color) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper: Color for range minimum.
setColorRangeMinimum(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Color for range minimum.
setColumnName(int, String) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Sets the header of column to specified string.
setCompactnessThreshold(double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Set the compactness threshold for eliminating non compact components.
setCompression(String) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Set the compression type
setConcavityMaskSize(int) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Specify size of local mask for concavity calculations.
setCondition(Double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
setCondition(T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.ConditionalDistribution: Set the conditional variable
setCondition(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
setCondition(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
setCondition(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
setCondition(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
setConnectivity(MTBBorder2D.BorderConnectivity) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Set the connectivity.
setConnectivity(MTBBorder2D.BorderConnectivity) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Specify connectivity for extracted border pixels.
setConnectorIDs(long[]) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Set connector IDs.
setContours(MTBContour2DSet) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator: Specify optional input contours.
setContourType(ContourOnLabeledComponents.ContourType) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Set reference to the contour type.
setCopyInputImage(boolean) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Enable/disable copy of input image.
setCorrectGamma(Boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Set flag to use gamma correction.
setCorrectPosition(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify if to correct line positions.
setCorrelationThreshold(double) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Set threshold for thresholding wavelet correlation images
setCountMode(CalcStructureStatistics.StructureCountMode) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Specify mode how to assign structures to cells.
setCovariance(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
setCreateBinaryMasks(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Enable/disable creation of binary masks.
setCreateColorImageFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Set the flag that determines the creation of an image with randomly colored regions.
setCreateIDImageFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Enable/disable creation of ID image.
setCreateLabelImageFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Set the flag that determines the creation of an image with region labels.
setCSVFile(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter: Specify the file where to save csv data.
setCurrentSlice(MTBImageManipulator) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Copy the values of the source to the current slice
setCurrentSliceCoords(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the current slice for functions that work on a slice only (this has nothing to do with the ij.ImageStack's current slice)
setCurrentSliceIndex(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the current slice for functions that work on a slice only (this has nothing to do with the ij.ImageStack's current slice) Stack indices range from 0 to N-1 (unlike ImageJ, where stack indices range from 1 to N)
setCurrentSliceLabel(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the slice label of the slice specified by the current slice index
setCurrentSliceLabel(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Set the slice label of the slice specified by the actual slice index
setCurrentSliceLabel(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Set the slice label of the slice specified by the actual slice index
setCurrentSliceLabel(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the slice label of the slice specified by the actual slice index
setCurrentZStackCoordinates(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the current z-stack coordinates for functions that work on (spatial) 3D only.
setCytoskeletonChannel(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Specify channel with stained cytoskeleton.
setDarkLine(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify if to detect dark lines on bright background.
setData(Vector<?>, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Set data for current MTBGraphEdge with the given cost.
setData(Vector<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Set data for current MTBGraphEdge.
setData(MTBTreeNodeData) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: Set the data object of the node.
setData(MTBDataExportableToImageJROI) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter: Specify the data to save.
setData(HashMap<String, HashMap<String, LinkedList<Double>>>) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Set the data to plot.
setData(HashMap<String, HashMap<String, Double>>) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Set the data to plot.
setDataIsPeriodic(boolean) - Method in class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D: Specify if data is periodic or not.
setDataset(double[][]) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Specify an input dataset.
setDebug(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Set value of debug.
setDebug(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of debug.
setDebug(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Set value of debug.
setDebug(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
setDebug(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
setDebug(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Set debug bit mask
setDefaultFps(int) - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane: Set a default fps to show in the option panel, e.g. if the fps can be determined from some image metadata
setDelimiter(ALDTableWindow.TableModelDelimiter) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Configure the delimiter to be used when exporting the table.
setDelta(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Set distance between threshold images to be compared.
setDeltaT(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
setDeltaT(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator: set the time between two frames
setDeltaX(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
setDeltaX(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator: set pixel length in x-direction
setDeltaX(Double) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
setDeltaXY(Double) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
setDeltaY(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
setDeltaY(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator: set pixel length in y-direction
setDeltaY(Double) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
setDeltaZ(Double) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
setDenoise(boolean) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Set the denoising flag. true to activate denoising.
setDestinationImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Set value of Input argument DestinationImage.
setDetectionChannel(int) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
setDetectionMode(CytoplasmAnalyzer2D.DetectMode) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Specify detection mode.
setDetector(ParticleDetectorUWT2D) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT: Specify particle detector to apply.
setDiagonalNeighbors(boolean) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: If true 8-neighborhood, i.e. diagonal neighbors, will be used in mode 'VORONOI_EXPAND' for Voronoi dilation.
setDiagonalNeighborsFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Set the neighborhood flag.
setDiameter(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
setDilateMaskSize(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Specify mask size for topology-preserving dilation.
setDirections(Vector<FeatureCalculatorHaralickMeasures.HaralickDirection>) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures: Directions to be analyzed.
setDistance(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures: Specify distance for calculating cooccurrence matrices.
setDistance(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures: Specify distance to be used in calculations.
setDistmet(DistanceTransform.DistanceMetric) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Specify the metric for the distance transformation.
setDistMetric(DistanceTransform.DistanceMetric) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Set the distance metric.
setDoErosion(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Set value of doErosion.
setDoGauss(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Specify if cell channel is to be smoothed prior to detection.
setDomainXMax(double) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Set maximal x value of user-specified domain.
setDomainXMin(double) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Set minimal x value of user-specified domain.
setDomainYMax(double) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Set maximal y value of user-specified domain.
setDomainYMin(double) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Set minimal y value of user-specified domain.
setDotGlobalAttributes(String[]) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter: Set global attributes of the graph e.g. the style of the nodes etc.
setDrawCurvatureInfoImage(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Enable/disable display of curvature info image.
setDrawSkeletonInfoImage(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Enable/disable display of skeleton info image.
setDrawType(DrawRegion2DSet.DrawType) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Set the kind of region image to be drawn
setEightconnected(boolean) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Set which neighborhood to use for labeling components.
setElementAt(MTBBorder2D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Set the i-th border of the set.
setElementAt(MTBContour2D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Set the i-th contour from the set.
setElementAt(MTBLineSegment2D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: Replace the i-th line segment of the set.
setElementAt(int, MTBPolygon2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Set a polygon at i-th position of the set.
setElementAt(MTBRegion2D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Set the i-th region from the set
setElementAt(MTBRegion3D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Set the i-th region from the set
setElementAt(MTBSurface3D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Set the i-th region from the set
setElementAt(int, MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Replaces the element at the specified position in this list with the specified element.
setElementAt(int, MTBNeurite2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet: Replaces the element at the specified position in this list with the specified element.
setEllipse(MTBQuadraticCurve2D) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Specify ellipse to draw.
setEndPixel(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Specify end pixel of path.
setEnergy(MTBGenericEnergyNonPDE) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of energy.
setEnergyList(Vector<MTBActiveContourEnergy>) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy: Sets list of energies.
setEnergyList(Vector<T>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: Specify a new set of energies, all weights are reset to 1.0.
setEnergyList(Vector<MTBActiveContourEnergy>) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Specify a new set of energies, all weights are reset to 1.0.
setEnergyList(Vector<MTBActiveContourEnergy>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable: Specify a new set of energies, all weights are reset to 1.0.
setEnergyList(Vector<MTBActiveContourEnergy>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable: Specify a new set of energies, all weights are reset to 1.0.
setEnergySet(MTBSet_ActiveContourEnergy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Specify set of energies.
setEnergySet(MTBSet_ActiveContourEnergy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
setEnergySet(MTBSet_ActiveContourEnergy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
setEqualWeightsFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Set the "equal weights"-flag
setErodeSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Set value of erodeSize.
setErodSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Set the size of the eroding element in pixel.
setESSPercentage(double) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA: Set percentage of number of samples used to determine if resampling is required, i.e. if it is below the current effective sample size (ESS).
setEstimateWidth(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify if to estimate width.
setExcluded(Vector<Integer>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
setExcludeList(int[]) - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans: Specify attributes to be excluded.
setExcludeMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Specify exclude mask.
setExcludeMask(boolean[][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Set exclude mask.
setExcludeMask(MTBImage) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
setExtendLine(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify if to extend lines.
setFactor(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
setFactoryMethod(MTBImage.FactoryMethod) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setFeatureOperators(Vector<FeatureCalculator>) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Set feature operators.
setFeatureType(FeatureCalculatorLBPJFeatureLib.FeatureType) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Specify type of features to be calculated.
setFG_Value(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing: set the intensity value of the remaining foreground regions
setFGOriginalValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Tell the thresholder to use the original pixel value for foreground pixels
setFGValue(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Set value of Parameter argument FGValue.
setFieldSizeX(int) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Set the field size in x-direction.
setFieldSizeY(int) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Set the field size in y-direction.
setFilename(String) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter: Set the filename for output
setFileName(String) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Set the filename of the image that has to be read.
setFileName(String) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Set image filename
setFill(Color) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
setFill(double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
setFilterImage(Boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Set flag to use gaussian filter.
setFilterMode(MedialnessMultiScaleFilter2D.FilterMode) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Set filter mode to define relation of foreground to background.
setFlagIsotropicCalculations(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures: Enable/disable isotropic calculations.
setFlagThrinkMatrix(boolean) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures: Flag for thrinking matrix if possible.
setForeground(DistanceTransform.ForegroundColor) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Set the foreground color.
setForwardTransform() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Toggle computation of the (forward) transform (image to wavelet)
setFps(Integer) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Set the frames per second for movie writers (*.avi,*.mov).
setFractionalDigits(int) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: specify the number of fractional digits for the results table
setFractionalDigits(int) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D: specify the number of fractional digits for the results table
setFrequency(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Specify frequency.
setGamma(Double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Set gamma correction value.
setGamma(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
setGamma(Double) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Set the gamma value.
setGammaToAuto(boolean) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Set if gamma should be calculated automatically or not.
setGaussianSigmaCurvatureSmoothing(double) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Set Gaussian standard deviation for smoothing curvature values.
setGaussSigma(double) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Specify sigma for Gaussian smoothing.
setGradientMode(GradientFieldCalculator2D.GradientMode) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Set the used gradient mode for field calculation.
setGraph(MTBGraph) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter: Set the main graph using MTBGraph
setGrayValue(Double) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Set the gray value of the regions in a mask image.
setGroundtruthObservations(Vector<MultiState<MotionModelID>>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
setGrownRegions(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
setH(double) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D: Set current h-parameter (max height of the h-domes).
setHaralickDirections(Vector<FeatureCalculatorHaralickMeasures.HaralickDirection>) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures: Set directions for which to calculate cooccurence matrices.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Set image height.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Set image height.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D: Specify height of filter mask.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D: Specify height of filter mask.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Specify height of filter mask.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Set image height.
setHighContrast(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify high contrast.
setHigherThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding: Specify higher threshold.
setHighQualityData(boolean) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Enable or disable extraction of high quality data.
setHistBins(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPs: Specify number of histogram bins.
setHistBins(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPsRIU: Specify number of histogram bins.
setHistBins(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Specify number of histogram bins.
setHistogram(MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
setHistoRegionSize(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Specify region for histogram binning.
setHistoryLink(Object, ALDPort) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess: Sets the port to which the object is to be linked in history.
setHSIInput(double[]) - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter: Specify HSI value to be converted.
setHueMTBImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Set the hue channel image.
setHueThresh(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
setID(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
setID(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Set the ID of the region.
setID(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: Set the ID of the region.
setID(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D: Set the ID of the region.
setIgnoreBorderFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Set flag to include/ignore structures along image border.
setIgnoreInvalidStackSpecification(boolean) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Set the flag to ignore an invalid stack specification.
setIgnoreMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Specfiy additional mask of pixels to ignore.
setIgnoreMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Specfiy additional mask of pixels to ignore.
setImageDir(ALDDirectoryString) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Specify input image directory.
setImageJPref(String, String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig: This functions sets a given property to the specified value.
setImagePart(MTBImageManipulator, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set a part of this image to the values of the source
setImagePlus(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox: Stores given image to the container.
setImageProcessor(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapter
setImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection: Set output image type.
setImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Set the resulting image's datatype.
setImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Set the image domain image
setInactive() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Set marker inactive.
setInConst(double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
setIndexOfImageToRead(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Set the index of the image that has to be read from the file.
setIndividually(boolean) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Set how to treat the components, individually or as a whole.
setInfo(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: Set info string of set.
setInfo(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
setInImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage: Specify input image.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Specify gray-scale input image.
setInImg(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Specify binary input image.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Set value of Input argument inImg.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology: Set input image for morphological operation.
setInImg(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Set the input image.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of inImg.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer: Set input image.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Set input image.
setInImg1(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
setInImg2(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
setInitalSegmentation(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
setInitBinImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of initBinImg.
setInitialSnakes(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Specify set of initial snakes.
setInitialSnakes(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Specify initial snakes.
setInitialSnakes(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Specify initial snakes.
setInitLabelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of initLabelImg.
setInitMask(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
setInitSegImageByte(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
setInner(Vector<MTBBorder2D>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Set the inner borders of the border object.
setInner(Vector<MTBBorder2D>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Set the inner contours of the contour object.
setInnerContourLengthMin(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Set the minimum number of pixels in the inner contour (length of the contour).
setInputArray(double[]) - Method in class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D: Set array to process.
setInputData(String, int[]) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper: Set input data.
setInputData(MTBTableModel) - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans: Specify input data.
setInputGrayScaleImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D: Specify input gray-scale image.
setInputGrayScaleImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos: Specify input gray-scale image.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor: Set input image to process.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Specify input image.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Specify input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Specify input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Set input image
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT: Specify input image to process.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Set the input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection: Set uneven illuminated input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Specify the input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Set low contrast input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.FeatureCalculator: Sets the input image to work on.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Set the underlying input image of the gradient field.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D: Set input image to analyze.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Specify the input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Specify input image.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Set input image to process.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Specify input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Set input image (if ConvexHullExtraction.inType is InputType.IMAGE).
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D: Set input image
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor: Set input image to process.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor: Set input image to process.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Set the input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Set input image.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Set reference to the current input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Set a new input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Set input image to process.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Specify an input image for the segmentation.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding: Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Set input image
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Set input image.
setInputImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet: Set input image into which to draw the contours.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Specify input image.
setInputImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet: Set input image into which to draw the polygons.
setInputImagePlus(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Set ImagePlus to store to disk
setInputImages(HashMap<Integer, ImagePlus>) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Setter for the input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Set input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Set input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Set input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Set input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter: Set input image
setInputLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D: Specify label input image.
setInputLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos: Specify label input image.
setInputLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Set input label image to process.
setInputMode(SegmentationInitializer.InputMode) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set input mode.
setInputMTBImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Set MTBImage to store to disk
setInputMTBImgRGB(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Set the input image.
setInputObservations(Vector<MultiState<MotionModelID>>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Set input regions (if ConvexHullExtraction.inType is InputType.REGIONS).
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Set input regions.
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Set reference to the the input regions.
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Set the input regions to be drawn.
setInputRegs(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Specify set of input regions.
setInputTreelines(HashMap<Integer, Vector<MTBRootTree>>) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator: Provide treelines to be enhanced.
setInputType(ConvexHullExtraction.InputType) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: Specify input image type.
setIntensityImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
setIntermediateLS(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
setIntermediateResultDirectory(String) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Set intermediate result directory.
setIntermediateResultPath(String) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Set path for intermediate results.
setInvalidImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of invalidImg.
setInvalidTilesNum(int) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult: Set number of invalid tiles.
setInverseTransform() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Set computation of the inverse transform (wavelet to image)
setInvert() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
setInvertMask(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D: Enable/disable inversion of mask.
setInvertMask(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Enable/disable inversion of mask.
setInvertMask(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D: Enable/disable inversion of mask.
setInvertMask(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Enable/disable inversion of mask.
setInvertPixelValues(boolean) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Enable/disable pixel values invertion.
setInvisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
setInvisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
setInvisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
setInvisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
setInvisible(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Set position (x,y) invisible.
setInvisible(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Set position (x,y,z) invisible.
setInvisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
setInvisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
setInvisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
setInvisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
setJmax(int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Set Jmax
setJmax(int) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Set Jmax (maximum scale 2^Jmax - 1)
setJmin(int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Set Jmin
setK(int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
setKernelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Set convolution kernel (image).
setKernelNormalization(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Set value of Parameter argument kernelNormalization.
setKernelOrigin(int[]) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter: Set value of Parameter argument kernelOrigin.
setKernelPart(GaborFilter2D.KernelPart) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Specify which kernel part should be generated.
setKernels(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Set smoothing kernels
setKernelSize(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Specify size of the kernel.
setKernelTruncation(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Set kernel truncation factor.
setKLower(int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
setKUpper(int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Set label image of detected nuclei.
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Set input label image.
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set the label image.
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage: Set Label image.
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Set image of region labels
setLabelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Set value of labelImg.
setLabelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Specify label input image.
setLabelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
setLambda(double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
setLambdaArray(double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
setLambdaArray(double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
setLayer(int) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Set the layer where the node is located.
setLength(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Specify length of vessels.
setLevel(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D: Set the tree level (level identifier).
setLineWidth(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify line width.
setLinkageMode(XylemGrower.GrowingMode) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
setLocation(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Set coordinates of current 3D point object.
setLocation(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D: Overwrites Java Point2D method.
setLocation(Point2D) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D: Overwrites Java Point2D method.
setLocation(Point2D.Double, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D: Sets the location of this SnakePoint2D to the same coordinates as the specified Point2D.Double object.
setLocation(double, double, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D: Sets the location of this SnakePoint2D to the specified double coordinates.
setLowContrast(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify low contrast.
setLowerThresh(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify lower threshold.
setLowerThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding: Specify lower threshold.
setMad(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Sets maximal allowed discrepancy of direct connection to actual profile between two peaks.
setMad(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Sets maximal allowed discrepancy of direct connection to actual profile between two peaks.
setMappingFile(String) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Specify mapping file.
setMarkerVectors(HashMap<Integer, CellCntrMarkerVector>) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Set currently available marker vectors.
setMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Specify binary mask of nuclei.
setMask(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Set optional exclude mask.
setMask(BasicMorphology.maskShape, int) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
setMask(MTBStructuringElement) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
setMaskDir(ALDDirectoryString) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Specify input mask directory.
setMaskFormat(CytoskeletonFeatureExtractor.CellMaskFormat) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Specify input mask format.
setMaskRadiusC(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Set value of Parameter argument maskRadiusC.
setMaskRadiusT(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Set value of Parameter argument maskRadiusT.
setMaskRadiusX(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Set value of Parameter argument maskRadiusX.
setMaskRadiusY(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Set value of Parameter argument maskRadiusY.
setMaskRadiusZ(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Set value of Parameter argument maskRadiusZ.
setMax_d2c(float) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Sets factor to adjust maximal allowed distance from lower to upper peak.
setMax_d2c(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Sets factor to adjust maximal allowed distance from lower to upper peak.
setMaxAngle(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Specify maximal angle to apply.
setMaxAreaChange(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
setMaxDistance(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
setMaximalComponentDistance(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Set maximal component/pixel distance for linking.
setMaximalComponentSize(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Set maximal component size for erasing large components.
setMaximalInstabilityScore(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Set maximal instability score.
setMaximalSize(long) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Set maximal size of valid regions.
setMaximalSpineLength(int) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor: Set maximal length of spines.
setMaximalSpineLength(int) - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor: Set maximal length of spines.
setMaximalVoronoiExpansionDistance(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Set radius of dilation mask in Voronoi expansion.
setMaximumObjectArea(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing: set the maximum area (number of pixels) a region must have in order to be kept
setMaxIter(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of maxIter.
setMaxIteration(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
setMaxIterations(int) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer: set maximum number of iterations for level set segmentation
setMaxIterations(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Set value of maxIterations.
setMaxLevels(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Specify maximum number of levels for iterative mode.
setMaxLineLength(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify maximal line length.
setMaxSpineLength(int) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Set maximum length of a spine (filopodia-like protrusion) in pixel.
setMaxWeight(double) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter: Specify the maximum weight in the graph.
setMean(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
setMeanFreeData(boolean) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Set flag to indicate if data is already mean-free.
setMeasure(ImageStatistics.StatValue) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats: Specify feature measure to extract.
setMeasurementUnit(SegResultEnums.MeasureUnit) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Specify unit for measurements.
setMeasureUnits(SegResultEnums.MeasureUnit) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Specify how to measure lengths and areas.
setMeasureUnits(SegResultEnums.MeasureUnit) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D: Specify units in which to measure areas.
setMeasureUnits(SegResultEnums.MeasureUnit) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Specify units in which to measure areas.
setMinAngle(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Specify minimal angle to apply.
setMinAreaAfterErosion(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
setMinAreaAfterOpening(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
setminAreaSeedRegions(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
setMinCompactness(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
setMinimalBorderLength(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Set the minimal border length.
setMinimalComponentSize(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Set minimal component size for erasing small components.
setMinimalCurvatureThreshold(double) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Set minimal curvature threshold.
setMinimalDiversity(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Set minimal diversity.
setMinimalLobeLength(int) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Set minimal pixel count a lobe requires.
setMinimalRegionSize(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Specify minimal size of regions considered.
setMinimalSize(long) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Set minimal size of valid regions.
setMinimumObjectArea(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing: set the minimum area (number of pixels) a region must have in order to be kept
setMinLineLength(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify minimal line length.
setMinRegionArea(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
setMinRegionSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Set the minimum size of detected regions.
setMinSeedSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
setMinSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Set value of minSize.
setMinSizeFraction(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Set value of minSizeFraction.
setMinTrackLength(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
setMinTrackLength(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator: set minimum track length
setMode(BasicMorphology.opMode) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
setModification(ImageValueTools.ImageValueModification) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
setMorphOp(BasicMorphology) - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection: Set morphological operation for illumination correction, default is closing.
setMTBImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox: Stores given image to the container.
setMultiphase(Boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of multiphase.
setNarrowBandWidth(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Set width of narrow band.
setNegativeColor(ArrayToColorMapImage.RangeColor) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: Color for negative values.
setNeighbourhood(XylemGrower.Neighbourhood) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
setNeurite(MTBNeurite2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
setNeuriteMaskSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Set neurite mask size in pixel.
setNeuriteSet(MTBNeurite2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D: Set the input set of neurites.
setNeuronColor(NeuriteExtractor2D.NeuronColor) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Set binary neuron color.
setNeuronImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Set input image of the binary neuron.
setNewObservations(AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
setNewObservations(AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
setNewObservations(AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
setNode(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData: Sets the node the object is associated with.
setNodeThreshold(double) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Set threshold for filtering nodes.
setNodeType(MTBNeuriteSkelGraphNode.MTBSkeletonNodeType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
setNormalizationMode(SnakeOptimizerSingle.EnergyNormalizationMode) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Set energy normalization mode.
setNormFromTo(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
setNormTo(double, double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
setNucDetector(NucleusDetector2D) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Set detector for nuclei.
setNucleiAvgSize(double) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Specify average size of nuclei.
setNucleiChannel(Integer) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Set nuclei channel number.
setNucleiCount(int) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Specify number of segmented nuclei regions.
setNucleiMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Specify nuclei mask.
setNucleiRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Specify set of regions.
setNucleiResult(SegResult_Nuclei) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Set nuclei detection result.
setNucleusChannel(int) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Specify image channel containing nuclei (just for reference).
setNumberNeighbors(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Specify number of neighbors to consider for LBP code calculation.
setNumberOfComponents(int) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Number of sub-space components if reduction mode is NUMBER_COMPONENTS.
setNumIterations(int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Set number of iterations for the GVF field.
setNumIterations(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of numIterations Explanation: Number of iterations performed
setNx(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
setNx(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
setNy(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
setNy(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
setObjectsEightConnected(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing: are regions to be considered 8-connected (4-connected otherwise)
setObjectsEightConnected(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
setOldId(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D: Set old index of current snake point within the snake.
setOpen() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Set polygon opened (not closed).
setOpeningSESize(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
setOperationType(FieldOperations2D.FieldOperation) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
setOpMode(NucleusSeparator2DBeamCut.NuclSeparateMode) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Set value of opMode.
setOrientedFilter(OrientedFilter2D) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Specify the oriented filter to apply.
setOutImageType(ImageReaderMTB.OutImageType) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Set the type of image object that is created as result image.
setOutOfRangeValueHandlingMode(GrayscaleImageToHeatmap.OutOfRangeValuesHandlingMode) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Specify how to handle values out of range.
setOutputDir(ALDDirectoryString) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Specify output directory.
setOutputFile(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter: Specify the file where to save the data.
setOutputType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter: Set output image type
setOverlapOpt(OverlapOption) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify overlap handling mode.
setOverwrite(boolean) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Set the overwrite permission flag
setParent(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode: Set the parent of this node.
setParentID(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
setPartChannel(Integer) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Set particle channel number.
setPartDetector(ParticleDetectorUWT2D) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Set detector for particles.
setParticle(int, G) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Set idx-th particle
setParticleImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D: Set particle image for particle detector.
setParticleResult(SegResult_Particles, int) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Set particle counts per channel.
setPath(String) - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData: Specify path associated with the node.
setPdf(int, ProbabilityDensityFunction) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
setPdf(int, ProbabilityDensityFunction) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
setPerCellAvgSize(HashMap<Integer, Double>) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Sets particle average sizes per cell.
setPerCellCount(HashMap<Integer, Integer>) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Sets particle counts per cell.
setPercentageOfVariance(double) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Fraction of variance to be represented in the sub-space if the reduction mode is PERCENTAGE_VARIANCE.
setPixelLength(double) - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Set length of a pixel.
setPoints(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
setPoints(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Set all points of the polygon from the specified point vector object.
setPoints(Vector<MTBPoint3D>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D: set points of this surface
setPoints(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Overwrite Polygon2D method to set all points of the snake from the specified point vector object.
setPointSet(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet: Set input set of 2D points.
setPointSet(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet: Set input set of 2D points.
setPoisson2Gauss(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Set flag if input image with poisson noise is to be transformed to image with gaussian noise following J.
setPositionC(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Set the window's position to 'c' in the c-dimension
setPositionT(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Set the window's position to 't' in the t-dimension
setPositionX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Set the window's position to 'x' in the x-dimension
setPositionY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Set the window's position to 'y' in the y-dimension
setPositionZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Set the window's position to 'z' in the z-dimension
setPositiveColor(ArrayToColorMapImage.RangeColor) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: Color for positive values.
setPrecursorInfosEnabled(boolean) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Enable or disable extraction of additional precursor infos.
setPredecessor(int) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
setPreserveTopology(Boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of preserveTopology.
setPreserveTopology(Boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Set value of preserveTopology.
setProcessMode(ComponentPostprocess.ProcessMode) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Specify process mode.
setProfile(double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile: Pass profile data to the profile.
setProfilePoints(Vector<Vector<Point2D.Double>>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile: Set the points of the neurite region where the profiles are calculated from.
setQuality(Integer) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Set the quality (quicktime only).
setRadius(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Set the radius of the node.
setRadius(int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator: Specify radius of local mask.
setRadius(double) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib: Specify radius of neighborhood for LBP code calculation.
setRandom(Random) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
setRandom(Random) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Set a random number generator to draw each region in a random color.
setRangeMaximum(double) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Specify maximum of heat map range.
setRangeMinimum(double) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Specify minimum of heat map range.
setRankOpMode(RankOperator.RankOpMode) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Set value of Parameter argument rankOpMode.
setReduceC(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Enable/disable projection along c-dimension.
setReduceT(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Enable/disable projection along t-dimension.
setReduceX(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Enable/disable projection along x-dimension.
setReduceY(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Enable/disable projection along y-dimension.
setReduceZ(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Enable/disable projection along z-dimension.
setReductionMode(PCA.ReductionMode) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Specify the mode for selecting the sub-space dimensionality.
setReductionMode(ImageDimensionReducer.ReducerMethod) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer: Specify projection mode.
setRegionBinaryMode(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Specify region input mode.
setRegionID(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Set the region id.
setRegionSet(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Set regions.
setRegionSet(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set the region set.
setREngine(Rengine) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Set R engine.
setResultCellImg(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Specify (optional) result image with cell contours.
setResultContourImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of ResultContourImage.
setResultDirs() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Create all output directories for the single detection steps.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D: Set the result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose: Set result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate: Set value of resultImg.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode: Set result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen: Set result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat: Set the result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of ResultImage.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D: Set the result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Set result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Set the resulting image.
setResultImageHeight(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Set target image height, overwrites all other internal settings.
setResultImageOffsetX(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Set desired offset for target image in x direction.
setResultImageOffsetY(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Set desired offset for target image in y direction.
setResultImagePlus(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Set resulting image
setResultImageStack(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Set stack with result segmentation images.
setResultImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
setResultImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
setResultImageWidth(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Set target image width, overwrites all other internal settings.
setResultImg(MTBImageShort) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos: Set value of resultImg.
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator: Set value of Output argument resultImg.
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter: Set result image
setResultingRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential: Attach the vector of resulting regions.
setResultMTBImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB: Set resulting image
setResults(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Set detected regions
setResultsTable(MTBTableModel) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
setResultType(GaborFilter2D.ResultType) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Specify result type.
setResultValueSelectionMode(ImageContrastReducer.ResultValueMode) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer: Set value selection mode.
setRevisionFile(String) - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile: Set the name of the revision file.
setROIFile(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter: Specify the ROI file to process.
setRoundnessThreshold(double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Set roundness threshold for eliminating round components.
setSampling(int) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Specify angular sampling.
setSatMTBImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Set the saturation channel image.
setSatTresh(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
setSaveIntermediateResultPath(String) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Set path where to save intermediate results.
setSavePath(String) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Sets the path to where intermediate snake results are to be written.
setSaveSnakes(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: (De)activates saving of iteration step results.
setScaleDown(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setScaleFactor(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE: set the scale factor if normalization is requested.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit: Set the scaling factor.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature: Set the scaling factor.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength: Set the scaling factor.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Set the scaling factor.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Set the scaling factor.
setScaleFactor(double) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable: Set the scaling factor.
setScaleFactor(double) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable: Set the scaling factor.
setScaleIntervalSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D: Set the size of the scale interval for correlation images
setScaleMax(Double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Set maximum of scales.
setScaleMin(Double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Set minimum of scales.
setScaleNum(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Set number of scales.
setScaleValues(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter: Set flag if values are scaled to match the range of output type values if necessary
setSeedImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
setSeedPointImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
setSeErosionSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
setSegDim(SegmentationInitializer.SegmentationDimension) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set target dimension.
setSegmentation(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Specifiy image segmentation.
setSegmentationDomain(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Specify the domain of the underlying segmentation.
setSeOpeningSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
setShape(CellCntrMarkerShape) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Set shape of marker.
setShape(SegmentationInitializer.ShapeType) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Specify shape for synthetic initialization.
setShapeDimX(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set extent of shape in x dimension.
setShapeDimY(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set extent of shape in y dimension.
setShapeDimZ(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set extent of shape in z dimension.
setShapeForErosion(BasicMorphology.maskShape) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
setShapeForOpening(BasicMorphology.maskShape) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
setShapeMaskSizeX(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set size of shape mask in x dimension.
setShapeMaskSizeY(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set size of shape mask in y dimension.
setShapeMaskSizeZ(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set size of shape mask in z dimension.
setShapePosX(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set position of shape in x dimension.
setShapePosY(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set position of shape in y dimension.
setShapePosZ(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set position of shape in z dimension.
setShowSnakes(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: (De)activates displaying of intermediate results during snake-iterations.
setSigma(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
setSigma(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify sigma value.
setSigma(double) - Method in class de.unihalle.informatik.MiToBo.math.arrays.filter.GaussFilterDouble1D: Set standard deviation of Gaussian kernel.
setSigmaC(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Set standard deviation (sigma) in c-dimension.
setSigmaInterpretation(GaussFilter.SigmaInterpretation) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Set the mode of how sigmas are interpreted.
setSigmaT(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Set standard deviation (sigma) in t-dimension.
setSigmaX(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Specify Gaussian standard deviation in x.
setSigmaX(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Set standard deviation (sigma) in x-dimension.
setSigmaY(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D: Specify Gaussian standard deviation in y.
setSigmaY(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Set standard deviation (sigma) in y-dimension.
setSigmaZ(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: Set standard deviation (sigma) in z-dimension.
setSizeC(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setSizeC(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Set standard deviation (size) in c-dimension.
setSizeDilation(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Set value of sizeDilation.
setSizeOpening(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Set value of sizeOpening.
setSizeT(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setSizeT(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Set standard deviation (size) in t-dimension.
setSizeTH(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Set value of sizeTH.
setSizeX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setSizeX(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Set standard deviation (size) in x-dimension.
setSizeY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setSizeY(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Set standard deviation (size) in y-dimension.
setSizeZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setSizeZ(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: Set standard deviation (size) in z-dimension.
setSlice(MTBImageManipulator, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Copy the value of source to the specified slice
setSliceLabel(String, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the slice label of the slice specified by (z,t,c)
setSliceZid(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator: Set index of slice in stack, starting with 0 for first slice.
setSnakeIterations(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Sets number of iterations for snake optimization.
setSnakePoints(Vector<MTBSnakePoint2D>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Set all points of the snake from the specified SnakePoint2D vector object.
setSource(MTBImageManipulator) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Set a new source for the window.
setSpacing(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of spacing.
setSpacingIntermediate(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE: Set value of spacingIntermediate.
setSrcNode(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Set source node of the MTBGraphEdge.
setStandardDeviation(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D: Specify standard deviation of Gaussian.
setStandardDeviation(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D: Specify standard deviation of Gaussian.
setStandardDeviation(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D: Specify standard deviation of Gaussian.
setStartFrame(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
setStartNode(MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Set a new start node.
setStartPixel(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Specify start pixel of path.
setState(int, Matrix, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState: Set the idx-th state (indices start from 0)
setState(int, Matrix, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
setStatus(byte) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Set the status of the node (segment).
setStepsizeT(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the stepsize in t-dimension (timestep)
setStepsizeT(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the stepsize in t-dimension (timestep).
setStepsizeX(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the physical size of a voxel (stepsize) in x-dimension
setStepsizeX(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the physical size of a voxel (stepsize) in x-dimension.
setStepsizeY(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the physical size of a voxel (stepsize) in y-dimension
setStepsizeY(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the physical size of a voxel (stepsize) in y-dimension.
setStepsizeZ(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the physical size of a voxel (stepsize) in z-dimension
setStepsizeZ(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the physical size of a voxel (stepsize) in z-dimension.
setString(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBStringData: Set the string data of the MTBStringData object.
setString(String) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage: Specify string.
setSuppressor(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Sets threshold to suppress peak analysis close to scraggy contours.
setSuppressor(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Sets threshold to suppress peak analysis close to scraggy contours.
setSVMFile(String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
setSVMParameters(svm_parameter) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
setT(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setTargetContrast(ImageContrastReducer.TargetContrast) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer: Set target contrast.
setTargetImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: Set target image.
setTargetImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Specify a target image to which the regions are drawn.
setTargetImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setTargets(Vector<CalcSegmentationStatistics.CalcTargets>) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: Specify targets to calculate.
setTgtNode(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Set target node of the MTBGraphEdge.
setTheta(Double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Set coefficient to relate vessel radius and scale.
setThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set threshold for threshold mode.
setThreshold(Double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE: Set value of threshold.
setThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Set threshold
setThresholdImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer: Set image for thresholding.
setThresholdingDirection(DetectMSERs.Thresholding_Direction) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Set direction of threshold compuations.
setThresTH(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: Set value of thresTH.
setTickLabelSize(int) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Set size of tick labels on both axes.
setTickLabelSize(int) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Set size of tick labels on both axes.
setTileShiftX(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Specify shift of tiles in x-direction.
setTileShiftY(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Specify shift of tiles in y-direction.
setTileSizeX(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Specify size of tiles in x-direction.
setTileSizeY(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Specify size of tiles in y-direction.
setTitle(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the image's title.
setTitle(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the images title
setTitle(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Set title of chart plot.
setTitle(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Set title of chart plot.
setType(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Set type of markers.
setU(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Set vector U of the field.
setU(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Set value on (x,y) for vector U of the field.
setUnitAngle(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator: set unit of angles
setUnitSpace(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator: set unit of space
setUnitT(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
setUnitT(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the unit of the t-dimension
setUnitT(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the unit of the t-dimension.
setUnitTime(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator: set unit of time
setUnitX(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the unit of the x-dimension
setUnitX(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the unit of the x-dimension.
setUnitXY(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
setUnitXY(String) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
setUnitXYZ(String) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
setUnitY(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the unit of the y-dimension
setUnitY(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the unit of the y-dimension.
setUnitZ(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the unit of the z-dimension
setUnitZ(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Set the unit of the z-dimension.
setup() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D: Initialize the class for the region
setupEnergyTable() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy: Inits the table for sampled energy values.
setupEnergyTable() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Inits the table for sampled energy values.
setupParamConfigPanel() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
setupParamConfigPanel() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
setUpperThresh(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Specify upper threshold.
setupWindow() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Construct the frame to configure an operator.
setUseThresh(Boolean) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D: Set adaptive thresholding tag.
setUWT(MTBImageSet) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Set UWT coefficient images
setV(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Set value on (x,y) for vector V of the field.
setV(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Set value on (x,y) for vector V of the field.
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel: Sets panel to given object value.
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel: Returns the contents of the text field.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
setValue(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel: Displays specified coordinates.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel: Sets panel to given object value.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
setValue(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage: Selects the given image object in combobox.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBWrapperDataIOSwing
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing
setValue(Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData: Set the value of the double datat object.
setValue(Integer) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData: sets the value for this object
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton: Updates GUI component with given value.
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Extracts current collection data.
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayButton: Updates GUI component with given value.
setValue(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Set new value.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
setValue(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton: Set new values.
setValue(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Updates current initializer configuration.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
setValueAt(Object, int, int) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
setVectorField(MTBVectorField2D) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Set the operation based 2D vector field.
setVectorFieldImage(MTBImageDouble) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Set the operation based 2D vector field image.
setVerbose(boolean) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
setVesselMode(MFFDOGFilter2D.VesselMode) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Specify detection scenario.
setVisibilityMask(boolean[][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Set the valid mask from external mask data.
setVisibilityMask(boolean[][][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: Set the valid mask from external.
setVisibilityMask(boolean[][], int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Set the valid mask from external mask data.
setVisible(boolean) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Set visibility of configuration window.
setVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
setVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
setVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
setVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
setVisible(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Set position (x,y) visible.
setVisible(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Set position (x,y,z) visible.
setVisible(boolean[][][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Set visibility of positions.
setVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
setVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
setVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
setVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
setVisualizeAnalysisResults(boolean) - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Enable/disable creation of image with analysis data.
setVoronoiImg(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile: Specify an image to be filled with voronoi data.
setVotesAdjacency(int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
setVotesClutter(int, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
setVotesTarget(int, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
setWeight(int, double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
setWeight(int, double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution: Set weight for particle specified by idx.
setWeight(int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
setWeight(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
setWeight(int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
setWeight(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
setWeight(int, int, double) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Sets the pixel weight of position (x,y) to c.
setWeight(int, int, int, double) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface: Sets the pixel weight of position (x,y,z) to c.
setWeight(int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
setWeight(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
setWeight(int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
setWeight(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
setWeight(PartitGraphNodeID, PartitGraphNodeID, double) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
setWeight(T, T, double) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix: Set weight of edge from nodeSrc to nodeTgt.
setWeightAsEdgeThickness(boolean) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter: Set flag how edge weights are visualized.
setWeightModel(DijkstraShortestPixelPathFinder.WeightModel) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Select model for choosing edge weights.
setWeights(double[]) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
setWeights(Vector<Double>) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy: Sets the weights for the energies.
setWeights(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: Specify new weights.
setWeights(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable: Specify new weights.
setWeights(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable: Specify new weights.
setWeights(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable: Specify new weights.
setWidth(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D: Set the width associated with the segment.
setWidth(int) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Set image width.
setWidth(int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Set image width.
setWidth(Double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Specify width of vessels.
setWidth(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Set image width.
setWindowPosition(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow: Set the window's position in the source image.
setWthMaskSize(Integer) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Set mask size of white top-hat.
setX(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
setX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setX(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Set coordinate of x-dimension.
setX(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Set x-coordinate of marker.
setXAxisLabel(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Set label of x-axis.
setXAxisLabel(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Set label of x-axis.
setXmax(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Set maximal x coordinate of region set domain.
setXmin(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Set minimal x coordinate of region set domain.
setXML(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Set the XML file description string if one was available
setXMTBImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Set the value channel image.
setXPos(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Set x-position of the node.
setXThresh(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Set the Intensity/Brighntness/Value-Parameter (depending on the used input image type).
setXylemImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Set the Hue/Saturation/{Intensity|Brightness|Value}-MTBImage.
setXylemImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: Set the input xylem image - this must be an 8bit image.
setXylemResultRegions(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Set the binary image after the morphological processing on the grown region image.
setY(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
setY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setY(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Set coordinate of y-dimension.
setY(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Set y-coordinate of marker.
setYAxisLabel(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Set label of y-axis.
setYAxisLabel(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Set label of y-axis.
setYmax(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Set maximal y coordinate of region set domain.
setYmin(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Set minimal y coordinate of region set domain.
setYPos(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Set y-position of the node.
setZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
setZ(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Set coordinate of z-dimension.
setZ(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: Set z-coordinate of marker.
setZTCCoordinates(int, int, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Specify optional coordinates if input image is a stack.
sgIDs - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Match list of set entries to original segmentation labels.
sgIDs - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Match list of set entries to original segmentation labels.
sgn(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Signum function.
sgn(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Returns the sign of a value.
sgnSum(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Computes scaled sign in neighborhood.
shape - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: (Optional) shape of marker.
shape - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
shape - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
ShapeAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
ShapeAnalyzer(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer: constructor
shapeDataAvailable() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Check if there is shape data available.
shapeDimX - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
shapeDimY - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
shapeDimZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
shapeForErosion - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: The shape of structuring element for the Erosion.
shapeForOpening - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: The shape of structuring element for the opening.
shapeIOShape - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to select shape.
shapeIOxDim - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to set x dimension of shape mask.
shapeIOxPos - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to set x position of shape.
shapeIOxSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to set size of shape in x.
shapeIOyDim - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to set y dimension of shape mask.
shapeIOyPos - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to set y position of shape.
shapeIOySize - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to set size of shape in y.
shapeIOzDim - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to set z dimension of shape mask.
shapeIOzPos - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to set z position of shape.
shapeIOzSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to set size of shape in z.
shapeMaskSizeX - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
shapeMaskSizeY - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
shapeMaskSizeZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
shapePosX - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
shapePosY - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
shapePosZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
shapeReport - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
shapeReport - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
ShapeType() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.ShapeType
shift(double, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Method to shift the whole polygon outward (positive value) ore inward (negative value) to its normal vector from every line segment.
shift(double, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Method to shift the whole snake outward (positive value) ore inward (negative value) to its normal vector from every line segment.
shiftX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Offset of the tiles in x dimension.
shiftY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Offset of the tiles in y dimension.
show() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Display the image as an ImagePlus.
showAboutBox() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
showAdditionalResultImages - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Flag to enable/disable showing additional and intermediate result images.
showAdditionalResultImages - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Flag to enable/disable showing additional and intermediate result images.
showAdditionalResults - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Enable/disable display of additional intermediate results.
showAdditionalResults - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules: Show additional result images.
showButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Button to show currently configured segmentation.
showCodeStack - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal: Show additional result image.
showContours(MTBImage, ArrayList<ArrayList<Point>>) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours: This method shows the contour pixel on a given image.
showDegreeTextbox() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
showDocuFrame() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame: Show the documentation for the chooser.
showHistogram(double[]) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
showIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Flag for showing intermediate results.
showIntermediateResults(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Set flag to display intermediate results.
showIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Flag for displaying intermediate results.
showIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
showIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Flag to enable/disable showing of intermediate results.
showKTextbox() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
showMaskChannelTextbox() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
showMaskChannelTextbox() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
showMasksOnly(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Set flag indicating whether to show masks or overlays in result stack.
showMaxDistTextbox() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
showMaxDistTextbox() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
showOverlayImage - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
showOverlayImage - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
showOverlayImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
showParametersForChecking() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
showResultFeatureStack - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Flag to enable/disable showing feature visualization stack.
showSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Display current result contour by overlaying the current snake result onto the input image.
showSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Display input image with current snake overlayed.
showSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Display intermediate results by overlaying the input image with the current snake result.
showSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Flag to enable/disable display of snake results.
showTrajectoryMap - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
showTrajectoryMap - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
showTrajectoryMap(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
sigma - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Sigma value of derivatives depending on line width.
sigma - Variable in class de.unihalle.informatik.MiToBo.math.arrays.filter.GaussFilterDouble1D: Standard deviation of the Gaussian kernel to be applied.
sigmaC - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
sigmaInterpretation - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
SigmaInterpretation() - Constructor for enum de.unihalle.informatik.MiToBo.filters.linear.GaussFilter.SigmaInterpretation
sigmaT - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
sigmaX - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
sigmaY - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
sigmaZ - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
signDistance(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Transform function into signed distance function.
signedExpandation(MTBLevelsetFunctionPDE.SortedList<MTBPoint3D>, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Expand signed distances around zero-level.
simplify() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Deprecated.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Get the number of borders of this set.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Get the number of contours of this contour set
size - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: number of bins
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet: Get the number of line segments in the set.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Get the number of polygons of this polygon set.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Get the number of regions of this region set
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag: Number of region sets in this bag
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Get the number of regions of this region set
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Get the number of regions of this region set
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet: Returns the number of elements in this list.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet: Returns the number of elements in this list.
size - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
sizeC - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
sizeC - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
sizeC - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
sizeC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
sizeC - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
sizeC - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
sizeDilation - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
sizeEnergy - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
sizeNeighborhood - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: The size of the neighborhood, i.e. numbers of pixels in the neighborhood
sizeOpening - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
sizePhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
sizesGT - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Array of sizes of groundtruth regions.
sizesGT - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Array of sizes of groundtruth regions.
sizesSG - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Array of sizes of segmented regions.
sizesSG - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Array of sizes of segmented regions.
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
sizeT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
sizeT - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
sizeT - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
sizeT - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
sizeTH - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Image width.
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
sizeX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
sizeX - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
sizeX - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
sizeX - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
sizeX - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
sizeX - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
sizeX - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Image height.
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
sizeY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
sizeY - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
sizeY - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
sizeY - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
sizeY - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
sizeY - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
sizeY - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
sizeZ - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
sizeZ - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
sizeZ - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
sizeZ - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
sizeZ - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
sizeZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
sizeZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
sizeZ - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
skeleton_color - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: The color of the skeleton in the binary image.
SkeletonAnalysisHelper - Class in de.unihalle.informatik.MiToBo.morphology: Helper functions for analyzing region skeletons.
SkeletonAnalysisHelper() - Constructor for class de.unihalle.informatik.MiToBo.morphology.SkeletonAnalysisHelper
SkeletonExtractor - Class in de.unihalle.informatik.MiToBo.morphology: Extracts skeleton of foreground region.
SkeletonExtractor() - Constructor for class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor: Default constructor.
skeletonInfoImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Info image for skeleton analysis.
SkeletonPostprocessor() - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor: Default constructor.
SkeletonPostprocessor - Class in de.unihalle.informatik.MiToBo.morphology: Helper operator to post-process binary region skeletons.
SkeletonPostprocessor() - Constructor for class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor: Default constructor.
skelImage - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Binary skeleton image of the whole neuron.
skelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Intermediate result: final contour skeleton.
skipLines - Variable in class de.unihalle.informatik.MiToBo.io.importer.GetMTBContour2DSetFromXSVFiles: Skip header lines.
smallestNonEmptyBin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: smallest intensity value contained in the input image
smoothContour(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Smoothes the contour by convolving x and y coordinates with a Gaussian kernel.
smoothPointVector(Vector<Point2D.Double>, double) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D: Convolves a list of 2D points with a Gaussian kernel.
snake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: The snake on which the algorithm works.
Snake_status() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer.Snake_status
snakeArea - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
SnakeCloner(MTBSnake) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner: Default constructor.
SnakeHelperOperators - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes: Helper class with internal operators for snakes.
SnakeHelperOperators() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators
SnakeHelperOperators.ContourConverter - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes: Operator class to convert a contour into a snake.
SnakeHelperOperators.ImageMaker - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes: Operator class to draw snake to an image.
SnakeHelperOperators.MaskMaker - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes: Operator class to generate 2D array mask for snake interior.
SnakeHelperOperators.RegionConverter - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes: Operator class to convert a region into a snake.
SnakeHelperOperators.RegionImageConverter - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes: Operator class to extract snakes from a region image.
snakeIterations - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Maximal number of snake iterations in iterative optimization.
snakeIterCount - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Number of snake iterations used in current optimization process.
snakeNum - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Number of snakes.
snakeNum - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty: Number of snakes to be optimized.
snakeNum - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Number of snakes currently managed.
snakeOpter - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D: Snake optimizer.
snakeOpters - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Array of individual snake optimizers.
SnakeOptimizer - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize: Image contour segmentation using parametric snakes.
SnakeOptimizer() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Default constructor
snakeOptimizer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Optimizer object for a single snake.
SnakeOptimizer.Snake_status - Enum in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize: Indicates the current (internal) state of the snake calculations.
SnakeOptimizerCoupled - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize: Image contour segmentation using multiple parametric snakes.
SnakeOptimizerCoupled() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Default constructor.
SnakeOptimizerCoupled(MTBImage, MTBPolygon2DSet, SnakeOptimizerSingle, boolean[]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Default constructor.
SnakeOptimizerSingle - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize: Image contour segmentation using parametric snakes.
SnakeOptimizerSingle() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Default constructor.
SnakeOptimizerSingle.EnergyNormalizationMode - Enum in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize: Snake normalization mode.
SnakeOptimizerSingle.IntensityNormalizationMode - Enum in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize: Image intensity normalization mode.
SnakeOptimizerSingleGreedy - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize: Image contour segmentation using parametric snakes with greedy optimization.
SnakeOptimizerSingleGreedy() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
SnakeOptimizerSingleVarCalc - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize: Image contour segmentation using parametric snakes.
SnakeOptimizerSingleVarCalc() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Default constructor.
SnakeOptimizerSingleVarCalc(MTBImage, MTBPolygon2DSet, MTBSet_SnakeEnergyDerivable, MTBGammaUpdate, Double, MTBTermination, Boolean, Double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Default constructor with parameters.
snakePrimerEllipse - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Set of elliptical snake polygons.
snakePrimerVoronoi - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Set of snake polygons based on Voronoi tesselation.
snakes - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch: Set of resulting contours.
solidities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
solve() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
solve() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Solve this level set problem.
SortedList() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList: create empty SortetList
SortedListElement(EType, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
SortMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.SortMode
sortRegionSetBy(MTBRegion2DSet, XylemGrower.SortMode) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
sortStringSet(Set<String>) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Helper method to sort set of strings alphabetically in ascending order.
sortStringSet(Set<String>) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Helper method to sort set of strings alphabetically in ascending order.
sourceObject - Variable in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
sp - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine: Start point of segment.
spacing - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
spacingIntermediate - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
spbox - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
splitFilename(String) - Static method in class cmdTools.mtb_imagetools.ImageConvert
SQRT_2 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2D2PNonPDE
SQRT_2 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DMPNonPDE
SQRT_2 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE
SQRT_3 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE
sqrtSizeMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
sqrtSizeMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
sqrtSizeMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
sqrtSizeMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
src - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Source node of the MTBGraphEdge.
stackedBarChart - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Resulting stacked bar chart.
StackedBarChartPlotter - Class in de.unihalle.informatik.MiToBo.visualization.plots: Operator that generates stacked bar plots using JFreeChart.
StackedBarChartPlotter() - Constructor for class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Default constructor.
stackedBarCharts - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Resulting stacked bar plot of cluster distributions.
stackedBarCharts - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Resulting stacked bar plot of cluster distributions.
stackSize - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Number of channels in image.
stageThreeMin - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Helper to make matrix minimum in stage three externally accessible.
standardization(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Get unit vector.
standardization(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
start - Variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime: Variable to save start value.
start - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
startC - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
startDetectionMode() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Method to start neurite detection mode with presegmentation, active contours and wavelet based neuron component detection.
startFrame - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
startPoint - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Start pixel of the path.
startPosOnContour - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Index of segment start pixel on contour.
startReal - Variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime: Variable to save real start value.
startT - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
startX - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
startY - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
startZ - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
stateConflict(Matrix, MultiState<MotionModelID>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
statesCont - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState: vector of the target states (continuous variables)
statesDiscr - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState: vector of the target states (discrete variables)
StatisticsFilter - Class in de.unihalle.informatik.MiToBo.filters.nonlinear: class for calculating several statistical values for the neighborhood of the pixels
in an image
StatisticsFilter() - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
StatisticsFilter(MTBImage, StatisticsFilter.FilterMethod, int) - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
StatisticsFilter.FilterMethod - Enum in de.unihalle.informatik.MiToBo.filters.nonlinear: available filtermodes
statMeasure - Variable in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats: Statistical measure to be calculated.
statMeasure - Variable in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult: Statistical measure to be calculated.
status - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: Status associated with the node.
status - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination: Status of current snake.
statuslabel1 - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
statuslabel2 - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
statusListeners - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D: vector of installed StatusListeners
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D: Vector of installed objects of type StatusListener.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer: Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: vector of installed StatusListeners
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: vector of installed StatusListeners
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D: Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
statusListeners - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
statusUpdated(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
statusUpdated(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
statusUpdated(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
statValue - Variable in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult: Result value, i.e. calculated statistical measure.
StatValue() - Constructor for enum de.unihalle.informatik.MiToBo.math.images.ImageStatistics.StatValue
stdDevConcavities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
stdDeviationFiltering(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
stdDevRatio - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement: Ratio of image standard deviation used as threshold for radius calculation.
StegerRidgeDetection2DWrapper - Class in de.unihalle.informatik.MiToBo.filters.vesselness: Wrapper for Ridge Detection plugin by Carsten Steger (and Thorsten Wagner).
StegerRidgeDetection2DWrapper() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Default constructor.
step() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Do one iteration, update all pixels of levelset function (in narrow band).
stepSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
stepSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Step size value for a snake step (gamma) during optimization.
stillActive - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor: Flag to indicate if process is still active.
str - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
stratifiedCrossValidation() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer: stratified k-fold cross validation, i.e. training and test tests contain approximately the same proportions of positive and negative samples in every iteration
StringAnalysis - Class in de.unihalle.informatik.MiToBo.tools.strings: Class providing helpers to analyze (sets of) strings.
StringAnalysis() - Constructor for class de.unihalle.informatik.MiToBo.tools.strings.StringAnalysis
stringToType(String) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: For a given String, return the corresponding MTBImageType.
StromulesDetector2D - Class in de.unihalle.informatik.MiToBo.apps.plantCells.stromules: Operator to detect stromules in microscope images of plastids.
StromulesDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Default constructor.
StromulesDetector2D.DetectMode - Enum in de.unihalle.informatik.MiToBo.apps.plantCells.stromules: Heuristic to use for detecting stromuli.
stromuliAngleThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Stromuli orientation angle criterion.
stromuliAngleThreshold - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules: Stromuli orientation angle criterion.
stromuliOp - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules: Operator for stromuli detection.
stromuliRegions - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Set of detected plastid regions with stromuli.
StructureCountMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics.StructureCountMode
structureMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics: Structure mask.
sub(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Method to sub two images.
sub(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics: Subtract the elements of two images (img1 - img2)
sub(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics: Subtract the elements two images (img1 - img2)
subDim - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA: Dimensionality of the sub-space as either specified by the user or automatically determined based on the percentage of variance.
subgraphEdges - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
subgraphID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID: The node's subgraphID
subgraphs - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
subgraphs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
subgraphs_adj - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
subgraphs_adj_color - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
subgraphs_color - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
subspaceData - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Dimension-reduced cluster distribution data.
subspaceData - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Dimension-reduced cluster distribution data.
sum - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: sum of all histogram entries
sumOfHueCartesian - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
sumSizeObject - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
supportConversion(Class<?>, Type[], Class<?>, Type[]) - Method in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
suppressor - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
surfaceAreas - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
SurfaceExtraction - Class in de.unihalle.informatik.MiToBo.features: Operator for extracting the surface areas of 3D-objects.
SurfaceExtraction() - Constructor for class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
SurfaceExtraction(MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
surfaces - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
surfaces - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
surfaceSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: The set of surfaces represented as a Vector.
svmFile - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
svmFile - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
swap(Point2D.Double[], int, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction: exchange point with index i and point with index j
swapNuclei - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
switchGapCloseMode() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Callback routine called if gap closing mode parameter changes.
switchOpModeParameters() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Callback routine to change operator mode parameters.
switchOpModeParameters() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Callback routine to change operator mode parameters.
switchOpModeParameters() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap: Callback routine to change operator mode parameters.
switchOpModeParameters() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping: Callback routine to change operator mode parameters.
switchPhaseConfigParameters() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Callback routine to change phase parameters.
switchPixelCalibParameters() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Callback routine called if pixel calibration mode parameter changes.
switchSegmentationFormatParameter() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Callback routine called if format parameter changes.
synchronizeColorOptions() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Updates color parameter if a random generator is given.
SynchronizedImageWindows - Class in de.unihalle.informatik.MiToBo.gui: A class that synchronizes viewing of images for easier comparison.
SynchronizedImageWindows() - Constructor for class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
synchronizeRandomOptions() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Updates random parameter if a color is set.

T

t - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
t - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
t1 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
t2 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
table - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
table - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
tableChanged(TableModelEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel
tableChanged(TableModelEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
tableChanged(TableModelEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow.MTBSet_SnkEnergyPDEGUITableModel
TableModelShowButton(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton: Constructor.
tableToString() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel: Converts the contents of the table to a string array in CSV format (suitable for import in Excel).
tabwin - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton: Associated window.
tail - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
targetClass - Variable in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
targetContrast - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer: Target contrast of result image.
TargetContrast() - Constructor for enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.TargetContrast
targetDimensionIO - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to read the target dimension.
targetEnergyRange - Static variable in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable: Target interval boundaries of energy.
TargetFormat() - Constructor for enum de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader.TargetFormat
TargetID - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl: A target-ID class.
TargetID(short) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID: Constructor.
targetIDtoIdx - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
targetImage - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage: Optional target image for result.
targetImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Optional target image.
targetImageType - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
targetList - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics: List of targets to calculate.
targetObject - Variable in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
tDirection - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs: Thresholding direction.
termCriterion - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc: Termination criterion.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff: Termination is done when the area difference of the former and the current snake is below a given fraction factor or if a maximum number of iterations is reached.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset: Termination is done when the area difference of the former and the current snake is below a given fraction factor or if a maximum number of iterations is reached.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination: Method to check termination status of the snake.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations: Termination is done when a maximum number of snake iterations is reached.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff: Termination is done when the snake control point motion of the former and the current snake is below a given fraction factor or if a maximum number of iterations is reached.
test(Vector<File>, int) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
testRegions(MTBRegion2D, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Test whether the number of pixels from a neuron region contains more than 90% of the pixels from a nucleus region.
testRegions2(MTBRegion2D, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Test whether a single pixel from a neuron region contains a pixel from a nucleus region.
text - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage: String to draw into the image.
textField - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel: Text field in the panel.
texturalEntropy - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
TexturalParameterExtractor - Class in de.unihalle.informatik.MiToBo.apps.biofilms: operator for calculating textural parameters from biofilm images as described in Yang et al., Quantifying biofilm structure using image analysis.
TexturalParameterExtractor() - Constructor for class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
TexturalParameterExtractor(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
tf - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
tgt - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge: Target node of the MTBGraphEdge.
theta - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
THREE_COMPONENTS_COLOR_SPACE - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
threshDWTCoeffs(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
threshDWTJeffreys(MTBImage[], double, double[]) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
threshHigh - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding: Upper threshold.
threshImage(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
threshImgNiblack(MTBImage, double, int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
threshLow - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding: Lower threshold.
threshold - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D: Higher threshold for binarization.
threshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
threshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
threshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu: Result threshold.
threshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
threshold(MTBImage, double, double, double, double, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Apply threshold to an MTBImage and create a new thresholded MTBImage.
threshold(MTBImage, MTBImage, double, double, double, double, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: Apply threshold to an MTBImage and write results to a destination MTBImage.
thresholdImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Thresholding_Direction() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs.Thresholding_Direction
thresholdIOImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to read an image for thresholding.
thresholdIOThresh - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: I/O component to read a threshold.
thresholdUnits - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Units for size thresholds.
threshScalingConstant - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D: Threshold scaling constant.
thresTH - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
thrinkMatrix - Variable in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures: Flag for thrinking matrix if possible.
tickLabelSize - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Size of axes' tick labels.
tickLabelSize - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Size of axes' tick labels.
ticks - Variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime: Variable to remember ticks.
tif - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
tiff - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
tileColumns - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Number of tile columns.
TileFeatureCalculator - Class in de.unihalle.informatik.MiToBo.features: Calculates features on images tile-wise, based on operators extending FeatureCalculator.
TileFeatureCalculator() - Constructor for class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Default constructor.
TileFeatureCalculator(int, int) - Constructor for class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Constructor with non-default tile sizes.
TileFeatureCalculator(int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Constructor with non-default tile sizes.
TileFeatureCalculatorResult - Class in de.unihalle.informatik.MiToBo.features: Result data of the operator TileFeatureCalculator.
TileFeatureCalculatorResult() - Constructor for class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult: Default constructor.
TileIterator(MTBImageTileAdapter) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator: Default constructor.
tileNumX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorEigenStructures: Number of tiles in x-dimension.
tileNumX - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Number of tiles in x dimension.
tileNumY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorEigenStructures: Number of tiles in y-dimension.
tileNumY - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Number of tiles in y dimension.
tileRows - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Number of tile rows.
tileShiftX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Tile shift in x-direction.
tileShiftX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Tile shift in x-direction.
tileShiftX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Tile shift in x-direction.
tileShiftX - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Shift of tiles in x direction.
tileShiftY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Tile size in y-direction.
tileShiftY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Tile size in y-direction.
tileShiftY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Tile size in y-direction.
tileShiftY - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Shift of tiles in y direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Tile size in x-direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Tile size in x-direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Tile size in x-direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Size of a tile in x-dimension.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Size of tiles in x direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter: Size of tiles in x dimension.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D: Tile size in y-direction.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D: Tile size in y-direction.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor: Tile size in y-direction.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter: Size of a tile in y-dimension.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator: Size of tiles in y direction.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter: Size of tiles in y dimension.
time - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID: A variable to store time information
timeLib - Static variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime: Basename of the JNI library.
timeOffset - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
timer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Timer object for time measurements.
timing - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: Consumed time in seconds where TimingMode states if this reflect user or real time.
timingMode - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: Timing mode, may be user time or real time.
titleString - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Title string of window.
tmpImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut: temp. binary image
tn - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
TNclutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
toArray() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
toByteImage() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Draw the skeleton graph into a binary image.
toCartesianAsPoint2D(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Converts an angle in degree to its corresponding in cartesian coordinates.
toCartesianAsVector(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Converts an angle in degree to its correspondant in cartesian coordinates.
toImage() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Visualize the skeleton graph as RGB image.
toImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Draw the skeleton graph in the given RGB image.
toImage(Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Visualize the neurites skeleton graph as RGB image.
toImage(MTBImageRGB, Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Visualize the neurites skeleton graph in the given RGB image.
toInspectL - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
toMicrons(double, String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils: Convert a value of given space unit to microns.
toMTBImage(String, MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Draws border with all inner borders to a given image.
toMTBImage(String, MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Method to save a region with in a given MTBImage image.
toMTBImage(String, MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Method to draw and save the snake in a given MTBImage.
toMTBImageByte(String, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D: Draws a border with all inner borders to a binary image with given size.
toMTBImageByte(String, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Method to save the region on a binary image with specific width and height.
toMTBImageByte(String, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Method to save the region on a binary image with specific width, height and color.
toMTBImageByte() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Method to save all contours from the regions on a binary image with specific width and height.
toMTBImageByte(String, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Method to draw and save the snake in a binary image.
topHat1D(double[], int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
tophat_concave(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat: Apply a top hat operator to the image for concavity detection.
tophat_convex(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat: Apply a top hat operator to the image for convexity detection.
TopHatContrastEnhancement - Class in de.unihalle.informatik.MiToBo.enhance: This class enhances the contrast by top-hat operations, especially for gray value bright filed or DIC images.
TopHatContrastEnhancement() - Constructor for class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Standard constructor.
TopHatContrastEnhancement(MTBImageByte, Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: Constructor to create a new IlluminationCorrection object.
tophatMode() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.ImgTophat.tophatMode
topologicalNumber2DN4 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Helper object used in topology preservation.
topologicalNumber2DN8 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Helper object used in topology preservation.
topologyPreservation - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
topoNumber2D - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
topoNumberIsOne(int[][][], int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: Check if topological for the class c is one in the neighborhood nbClassess3D.
topoNumberIsOne(MTBSegmentationInterface, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: Check if topological for the class c is one in the pixel with coordinate (x,y,z) in the segmentation object segmentation.
topoNumberIsOne(int[][][], int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2D
toPositiveAngle360(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Simple way to convert negative angles to 0-360 degree.
toPositiveAngle360(double) - Static method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Normalize angles (in the range -360 to 360 degree) to the range 0-360 degree.
toRGB() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter: Method to convert colors from HSV color space to RGB color space.
toRGB(double, double, double) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter: Method to convert a single color from HSV color space into RGB color space.
toSeconds(double, String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils: Convert a value of given time unit to seconds.
toString() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputData
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Returns the String "IMG("title of the image")"
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
toString() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Return an ascii representation identifying the energy and internal parameters, but not the state.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership: Return a string representation.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
toString() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable: Get an identifier string for the energy object.
toString() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable: Get an identifier string for the energy object.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate: Method for short adaptation description name.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination: Method for short termination description name.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
toString() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
toSWC(String, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Method to save neurite skeleton graph as SWC file.
totalAreas - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
totalLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Total length of indentation or protrusion, i.e., equals the sum of MorphologyAnalyzer2DInProData.InProContourSegment.basalLength and MorphologyAnalyzer2DInProData.InProContourSegment.apicalLength.
totalNumberOfObjects - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
totalObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency: total number of observations over all frames
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Convert contour object to MTB XML datatype.
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Generate xml-representation of this 3D-point.
toXMLType(MTBXMLPolygon2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Convert object to XML representation.
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Create a xml representation of this polygon set using MiToBo's xml-scheme MTBXMLPolygon2DSet.xsd
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D: Construct an object that represents this region by xml.
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Construct an object that represents this region by xml.
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag: Create a xml representation of this bag of region sets using MiToBo's xml-scheme MTBRegion2DSetBag.xsd
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Construct an xml-representation of this set of 3D-regions.
toXMLType(MTBXMLSnakeType) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Convert object to XML representation.
toXMLType(Matrix) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter: Convert a JAMA matrix to its xml-beans type
toXMLType(MultiState<MotionModelID>) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter: Convert a MultiState object to its xml-beans representation
toXMLType(Vector<MultiState<MotionModelID>>) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter: Convert a Vector> object to its xml-beans representation
toXMLType() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID: Convert this object to its XML-representation.
tp - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
tp - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc: True positives.
tp - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc: True positives.
TPclutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
TPtrackend - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
TPtracksegment - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
TPtrackstart - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
traceBranch(MTBImage, int, int, MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Traces a skeleton branch and extracts its length.
traceBranch(MTBImageByte, Vector<Point2D.Double>, Point2D.Double) - Static method in class de.unihalle.informatik.MiToBo.morphology.BinaryImageEndpointTools: Continues a given branch at the given pixel recursively.
traceBranch(MTBImage, int, int) - Static method in class de.unihalle.informatik.MiToBo.morphology.SkeletonAnalysisHelper: Traces a skeleton branch and returns the list of its pixels.
traceContour(int, int, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Trace contour, starting at (xS, yS) in direction dS.
track() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite: the actual tracking method
TrackAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D: class for analyzing movement and shape of already tracked objects in a given label image
TrackAnalyzer(Vector<Trajectory2D>) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
trackcolors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
trackcolors - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
trackerOutputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
trackEvalResult - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
TrackEvaluator - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
TrackEvaluator(Vector<MultiState<MotionModelID>>, Vector<Vector<MultiState<MotionModelID>>>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
TrackEvaluator.TrackEvaluatorResult - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
TrackEvaluator.TrackObservation - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
TrackEvaluator.TrackSegment - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
TrackEvaluatorResult() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
trackgraphs - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
trackImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
trackingtime - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult: time that elapsed for tracking
TrackObservation(int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
trackReport - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
trackReport - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
tracks - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo: HashMap of the tracks represented by the sample.
TrackSegment(int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
TrackVisualizer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
TrackVisualizer(MTBImage, Vector<Trajectory2D>) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
trafo - Variable in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
train() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer: the actual svm training
trajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
trajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
trajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
trajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
Trajectory2D - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
Trajectory2D(int, int, Vector<Point2D.Double>) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
Trajectory2D(int, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
Trajectory2D(int) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
TrajectoryExtraction2D - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
TrajectoryExtraction2D(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
transform(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise: Transform the (column) vector x and add noise sampled from the Gaussian noise distribution.
transform(GaussianDistribution) - Method in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise: Transform the Gaussian distribution gaussian with this transform.
transform(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D: Compute the h-dome transform
transform - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
TransformationMode() - Constructor for enum de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform.TransformationMode
translate(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Translate current coordinates of the 3D point object.
traversePolygonPointList(Vector<Point2D.Double>, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D: Helper function for simplify().
traverseSubdir(String, String) - Static method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree: Recursive traversal of subdirectories.
trim(Hashtable<Integer, Vector<Double>>, int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
truncate(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram: truncate the histogram to the specified interval
tSize - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Size of input image in t dimension.
TwoColumnPanel - Class in de.unihalle.informatik.MiToBo.gui: A panel with a titled border and two columns for a variable number of generic components that are placed vertically with an additional label.
TwoColumnPanel(String) - Constructor for class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel: Constructor
type - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
type - Variable in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException: Type of exception.
type - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InflectionPoint: Type of segment starting with this point.
type - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment: Type of segment.
type - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Type of the input image and later the type of the calculated 2D vector field.
type - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector: Type ID of markers.
type - Variable in exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException: Type of exception.
typeoftime - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult

U

U - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Vector U including the x-values of the vector field.
U - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: U-component-vector of the vector field.
UDE(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors: This method computes the underdetection error.
ulimits - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
UndecimatedWaveletTransform - Class in de.unihalle.informatik.MiToBo.transforms: Undecimated wavelet transform (UWT) operator.
UndecimatedWaveletTransform() - Constructor for class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Constructor with default Gaussian kernel [1/16, 1/4, 3/8, 1/4, 1/16] for dimension x, y and z, no image and denoise set to false.
UndecimatedWaveletTransform(MTBImage, int, boolean, MTBImage[]) - Constructor for class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Constructor.
UndecimatedWaveletTransform(MTBImage, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Constructor with default Gaussian kernel [1/16, 1/4, 3/8, 1/4, 1/16] for at most dimension x, y (and z if present).
UndecimatedWaveletTransform(MTBImage, int, boolean, boolean) - Constructor for class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform: Constructor with default Gaussian kernel for sd = 1 [1/16, 1/4, 3/8, 1/4, 1/16] for at most dimension x, y (and z if present) or sd=0.5 [0.0002638651, 0.1064507720, 0.7865707259, 0.1064507720, 0.0002638651] if sigmaEqualsOne is false
UndecimatedWaveletTransform.TransformationMode - Enum in de.unihalle.informatik.MiToBo.transforms
UniformDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl: A multivariate uniform distribution.
UniformDistribution(int, double[], double[], Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution: Constructor for uniform distribution with hypercube shape in dimension DOF, given lower and upper limits in the corresponding dimension and a random generator for sampling.
unitAngle - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
units - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D: Units used in measurements, default is pixels.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete: Unit in which measurements are provided.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm: Unit in which measurements are provided.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei: Unit in which measurements are provided.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles: Unit in which measurements are provided.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel: Unit in which measurements are provided.
unitSpace - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
unitT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
unitT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
unitT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
unitTime - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
unitVector(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Return the unit vector of vector.
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Physical pixel size units.
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
unitXY - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
unitXYZ - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
unsetActualSliceOnly() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh: The whole image is thresholded (default)
unsetAssociation(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive: Unsets the association of the specified observation and state.
unsetAssociation(int, int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation: Unset the association between target and observation.
UNTITLED - Static variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Title string for new and untitled images
update(AbstractMultiState<MotionModelID>, DataAssociation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
update(T, DataAssociation) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetPredictionFilter: Update step method given a multi-target observation
update(AbstractMultiState<T>, DataAssociation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA: The DataAssociation object may be null and is interpreted as groundtruth if given.
update(LinearTransformGaussNoise, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
updateAndRepaintWindow() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Update and repaint the image window if the image is displayed by ImageJ
updateButtonColor(Color) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel: Update the button icon with the given color.
updateGUI() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.
updateIDs(Vector<MTBSnakePoint2D>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Update method for snake point ID's after make snake simple.
updateImageAndColorSettings() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Updates output image type and gray values according to chosen draw type.
updateImageList(String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage: Updates image list and GUI.
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Should be used to create or update ImagePlus data if the MTBImage is not using an ImagePlus to store the data (MTB_INT, MTB_DOUBLE, MTB_RGB).
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte: Does nothing, because the underlying ImagePlus is updated immediately when values are changed in the MTBImage
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble: Creates or updates an ImagePlus of Float type from the MTBImage Double data, can be returned by getImagePlus() or displayed by show()
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat: Does nothing, because the underlying ImagePlus is updated immediately when values are changed in the MTBImage
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt: Creates or updates an ImagePlus of Float type from the MTBImage Int data, which can be returned by getImagePlus() or displayed by show()
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB: Creates or updates an ImagePlus of RGB type from the MTBImage RGB(3 byte-channels) data, can be returned by getImagePlus() or displayed by show()
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort: Does nothing, because the underlying ImagePlus is updated immediately when values are changed in the MTBImage
updateImageSize_ImgToProp() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Update the image size in the properties hashtable from the image's size
updateIndep(int, LinearTransformGaussNoise, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
updateIndep(int, int, LinearTransformGaussNoise, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians: Update i-th Gaussian component with j-th observation
updateOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled: Update current overlap mask for all snakes.
updateParameters(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit: Updates parameters according to given membership.
updateParameters(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep: Updates internal parameters according to given segmentation.
updateParams(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
updateParams(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
updateParams(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
updateParams(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
updateParams(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
updateParams(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
updateParams(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Update parameters (if any) of the energy object which depend on the associated level set function.
updateParams(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE: Update parameters (if any) of the energy object which depend on the associated level set function.
updateParams(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
updateParams(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
updatePhysProperties_ImgToProp() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Update physical properties (stepsizes, units) in the properties hashtable from its member variables
updatePhysProperties_PropToImg() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: Update physical properties (stepsizes, units) of the image (member variables) from its properties hashtable
updateRegions() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D: Update neurite shaft and growth cone regions, due to changes of this regions by adding features or something else.
updateSnakeSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Convenience function for updating the segmentation.
updateStatus(MTBLevelsetFunctionDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
updateStatus(MTBLevelsetFunctionDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
updateStatus(MTBLevelsetFunctionDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
updateStatus(MTBLevelsetFunctionDerivable) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable: Function which updates the internal status of the energy.
updateStatus(SnakeOptimizerCoupled) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
updateStatus(SnakeOptimizerCoupled) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
updateStatus(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable: Update internal state of energy object prior to querying derivatives and so on.
updateStatus(SnakeOptimizerCoupled) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCoupled: Update internal state of energy object prior to querying derivatives and so on.
updateStatus(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable: Update internal state of energy object prior to usaging it.
updateTable() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult: Updates the result table as new data is added.
updateTargetImageDependencies() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet: Updates parameters depending on the target image.
upperBound - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
upperThresh - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper: Pixels with a response above this threshold are immidiately accepted.
upperThreshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
useAngleCriterion - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Enable/disable angle criterion.
useAngleCriterion - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules: Enable/disable angle criterion.
useAutoDistance - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
useAutoDistance - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
useAutoDistanceDetermination(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
useAutoGamma() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D: Callback routine to change parameters.
useEllipseDistThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Enable/disable ellipse distance threshold.
useEllipseDistThreshold - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules: Enable/disable ellipse distance threshold.
useExternalSVM - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
useExternalSVM(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
useGammaCorrection() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Callback routine to change parameters.
useHeavideApproximation(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
useHeavideApproximation(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
useHeavideApproximation(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
useHeavideApproximation(boolean) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable: Enable or disable approximation of Heaviside function.
useHeavisideApprox - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area: Flag to indicate if the Heaviside function should be approximated.
useHeavisideApprox - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit: Flag to indicate if the Heaviside function should be approximated.
useHeavisideApprox - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length: Flag to indicate if the Heaviside function should be approximated.
useJNI - Variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime: Does this instance use JNI and thus user time?
useMask - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
useMultiIntersectionCheck - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Enable/disable line multi-intersection check.
useMultiIntersectionCheck - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules: Enable/disable line multi-intersection check.
UserTime - Class in de.unihalle.informatik.MiToBo.tools.system: This is a stopwatch to measure elapsed user or real time used.
UserTime() - Constructor for class de.unihalle.informatik.MiToBo.tools.system.UserTime: Creates a new time object and starts the clock.
UserTime(boolean) - Constructor for class de.unihalle.informatik.MiToBo.tools.system.UserTime: Creates a new time object and starts the clock elapsing real time.
useSpecifiedDomain - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader: Flag for using user-specified domain information.
useThresh - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
uwt - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D.UWTRunner: Reference to (external) UWT operator.
uwtImages - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
UWTRunner(UndecimatedWaveletTransform) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D.UWTRunner: Default constructor.

V

v - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter: Array of intensity values.
v - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter: Intensity of HSV space.
V - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Vector V including the y-values of the vector field.
V - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: V-component-vector of the vector field.
valid(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable: Validity of point (x,y,z).
valid(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: is this pixel valid?
validate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
validate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
validate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
validate() - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable: Function to validate configuration of energy object.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D: Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D: Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D: Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D: Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
validateCustom() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
validateCustom() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
validateCustom() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
validateCustom() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
validateCustom() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBP
validateCustom() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIU
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter: The validation of parameters and inputs.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter: The validation of parameters and inputs.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
validateCustom() - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
validateCustom() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
validateCustom() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
validateCustom() - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet
validateCustom() - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet
validateCustom() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
validateCustom() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
validateCustom() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.CropImage
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
validateSeedTextField() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
ValidationMethod() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ValidationMethod
validColor - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
validMultiState(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory: Test if the specified multistate is valid for this factory.
value - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData: Double value for these object.
value - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
value(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.ResponseDifference
value - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.BorderBackgroundContrast: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.GapCloseMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.ImageType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.LobeTypes: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.MeasurementUnits: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.OperationMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.OperatorPhasesToRun: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.PixelCalibration: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationInputFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D.BorderBackgroundContrast: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D.OperationMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D.DetectMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor.CellMaskFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete.SegmentationMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResultEnums.MeasureUnit: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator.LayerSubset: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator.OpWorkingMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing.DrawType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing.ROOTSEGMENT_STATUS: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D.NeuriteDetector2DMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos.DetectorExternalEnergy: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D.NeuronColor: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D.NuclDetectMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D.ResultImageMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut.NuclSeparateMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D.ResultImageMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D.DetectMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.AbsenceDetectionMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.ScratchOrientation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.KERNEL_TYPE: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ScratchOrientation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ValidationMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.Neighbourhood: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.SortMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.Mode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.InputMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.OutputMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.FactoryMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow.BoundaryPadding: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D.BorderConnectivity: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode.MTBSkeletonNodeType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.CurveType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException.DatatypeExceptionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader.TargetFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator.Algorithm: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D.FeatureNames: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.SegmentType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer.FeatureNames: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures.HaralickDirection: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib.FeatureType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal.NeighborhoodSelection: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.fields.FieldOperations2D.FieldOperation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D.GradientMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.KernelPart: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.ResultType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D.ApplicationMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer.JoinMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.GaussFilter.SigmaInterpretation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator.RankOpMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter.FilterMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D.FilterMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D.VesselMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.VesselMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB.OutImageType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder.WeightModel: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.images.ImageArithmetics.ArithOp: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.images.ImageStatistics.StatValue: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm.ScoreInterpretation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.statistics.PCA.ReductionMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.maskShape: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.opMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess.ProcessMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction.InputType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.DistanceMetric: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.ForegroundColor: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.ImgTophat.tophatMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException.ExceptionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics.CalcTargets: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface.SegmentationDimension: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.InputMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.SegmentationDimension: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.ShapeType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents.BorderType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents.ContourType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics.StructureCountMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper.ApproxVersion: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE.VelocityExpansionMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs.Thresholding_Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer.Snake_status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.EnergyNormalizationMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.IntensityNormalizationMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu.InputType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack.Mode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.ResultValueMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.TargetContrast: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.ReducerMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageValueTools.ImageValueModification: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.AType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform.TransformationMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage.RangeColor: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap.OperationMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap.OutOfRangeValuesHandlingMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping.IgnoredValuesHandlingMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping.OperationMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet.DrawType: Returns the enum constant of this type with the specified name.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.BorderBackgroundContrast: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.GapCloseMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.ImageType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.LobeTypes: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.MeasurementUnits: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.OperationMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.OperatorPhasesToRun: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.PixelCalibration: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationInputFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D.BorderBackgroundContrast: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D.OperationMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D.DetectMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor.CellMaskFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete.SegmentationMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResultEnums.MeasureUnit: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator.LayerSubset: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator.OpWorkingMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing.DrawType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing.ROOTSEGMENT_STATUS: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D.NeuriteDetector2DMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos.DetectorExternalEnergy: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D.NeuronColor: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D.NuclDetectMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D.ResultImageMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut.NuclSeparateMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D.ResultImageMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D.DetectMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.AbsenceDetectionMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.ScratchOrientation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.KERNEL_TYPE: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ScratchOrientation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ValidationMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.Neighbourhood: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.SortMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.Mode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.InputMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.OutputMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.FactoryMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow.BoundaryPadding: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D.BorderConnectivity: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode.MTBSkeletonNodeType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.CurveType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException.DatatypeExceptionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader.TargetFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator.Algorithm: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D.FeatureNames: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.SegmentType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer.FeatureNames: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures.HaralickDirection: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib.FeatureType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal.NeighborhoodSelection: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.fields.FieldOperations2D.FieldOperation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D.GradientMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.KernelPart: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.ResultType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D.ApplicationMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer.JoinMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.GaussFilter.SigmaInterpretation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator.RankOpMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter.FilterMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D.FilterMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D.VesselMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.VesselMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB.OutImageType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder.WeightModel: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.images.ImageArithmetics.ArithOp: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.images.ImageStatistics.StatValue: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm.ScoreInterpretation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.statistics.PCA.ReductionMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.maskShape: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.opMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess.ProcessMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction.InputType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.DistanceMetric: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.ForegroundColor: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.ImgTophat.tophatMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException.ExceptionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics.CalcTargets: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface.SegmentationDimension: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.InputMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.SegmentationDimension: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.ShapeType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents.BorderType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents.ContourType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics.StructureCountMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper.ApproxVersion: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE.VelocityExpansionMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs.Thresholding_Direction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer.Snake_status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.EnergyNormalizationMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.IntensityNormalizationMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu.InputType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack.Mode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.ResultValueMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.TargetContrast: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.ReducerMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageValueTools.ImageValueModification: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.AType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform.TransformationMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage.RangeColor: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap.OperationMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap.OutOfRangeValuesHandlingMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping.IgnoredValuesHandlingMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping.OperationMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet.DrawType: Returns an array containing the constants of this enum type, in the order they are declared.
var - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
varCheckNB - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Size of neighborhood for local variance checks.
varCheckThresh - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Threshold for variance check.
variance(Vector<Double>, double) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
varianceFiltering(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
vectorDiff(double[], double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Subtract two vectors.
vectorField - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: The 2D vector field for several operations.
vectorField - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: The resulting 2D vector field.
vectorField - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: The calculated GVF vector field.
VectorField2DPotentialFinder - Class in de.unihalle.informatik.MiToBo.fields: Routines for reconstructing potential from vector field.
VectorField2DPotentialFinder() - Constructor for class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder: Standard constructor.
VectorField2DPotentialFinder(MTBVectorField2D) - Constructor for class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder: Default constructor.
VectorField2DPotentialFinder.PotentialFinderOptFunction - Class in de.unihalle.informatik.MiToBo.fields: Optimization function for gradient-based potential reconstruction.
vectorFieldImage - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: The 2D vector field stored to an image.
vectorFieldImage - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: The resulting 2D vector field stored to an image.
vectorFieldImage - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression: Image with input 2D gradient field.
vectorNorm(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Returns the norm of a vector.
vectorOfCurvatures - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator: Resulting Curvatures for each Pixel on the given MTBContour2D.
vectorSum(double[], double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper: Sums up two vectors.
vectorToString(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
vectorToString(int, Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
VelocityExpansionMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE.VelocityExpansionMode
verbose - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Verbose flag for standard console outputs.
verbose - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess: If true, verbose outputs are written to standard output.
verbose - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
verbose - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
verbose - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate: Flag to turn display of additional information on/off.
verbose - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination: Flag to turn display of additional information on/off.
verbosePrintln(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter: prints the given text if the verbose flag is set
verbosePrintln(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite: prints the given text if the verbose flag is set
version - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper: Type of approximating function to use.
vesselImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Result of vesselness detection (for internal use only).
vesselImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Intermediate result: vesselness image.
VesselMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D.VesselMode
VesselMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.VesselMode
vExpandMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
vidpanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
visibilityMapHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Height of visibility map.
visibilityMapWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Width of visibility map.
visible - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Visibility array.
visiblemap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Visibility map for hiding individual pixels.
visiblemap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: Visibility map for hiding individual pixels.
visiblemap - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Visibility map for hiding individual pixels.
visibleMapMaxX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Maximal x coordinate of visibility map.
visibleMapMaxY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Maximal y coordinate of visibility map.
visibleMapMinX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Minimal x coordinate of visibility map.
visibleMapMinY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake: Minimal y coordinate of visibility map.
visitCC(int, int, int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: Visit (x,y,z): reset the corresponding entry in X to false and recursively visit all neighbors of (x,y,z) in X.
visitNeighboursOf(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D: Inspect the eight/four neighbours of the pixel with the given coordinate.
visualizeAnalysisResults - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Enable/disable the creation of an image to visualize results.
vol - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
volume - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D: The volume of the region (number of points included).
volumes - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
voronoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator: Function to extract Voronoi primers.
VoronoiExpandComponents(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess: Deprecated.
Implementation is quite slow, use method ComponentPostprocess.dilateComponentsTopologyPreserving(MTBImage, int).
voronoiImg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile: Image filled with voronoi tesselation data during profile calculation if non-null.
votesClutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
votesTarget - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
vx - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
vy - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer

W

w - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE: weight for neighbors
wantStackWithIntermediateResults(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer: Flag for turning on/off generation of stack with intermediate results.
WatershedBinary - Class in de.unihalle.informatik.MiToBo.morphology: Watershed transformation on binary images.
WatershedBinary() - Constructor for class de.unihalle.informatik.MiToBo.morphology.WatershedBinary: Default constructor.
WatershedBinary(MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.morphology.WatershedBinary: Constructor.
weightAsEdgeThickness - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
weightmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Map of weights for the segmentation.
weightmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: Map of weights for the segmentation.
weightModel - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Model for the edge weights.
WeightModel() - Constructor for enum de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder.WeightModel
weights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
weights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
weights - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline: Used as a substitute for the same field in MTBSet_???
weights - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy: List of energy weights.
whiteTophat(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology: calculates the white tophat transform, i.e. difference of image and the opening of the image
(also called opening tophat)
width - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant: Width of the input image.
width - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D: Width of the input image.
width - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
width - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos: Image size in x-direction, given in pixel.
width - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D: Width of the binary neuron image.
width - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
width - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D: Width of the processed image.
width - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D: Width of the segment (for compatibility with ImageJ).
width - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph: Skeleton image size in x-direction.
width - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D: Width of the image where the vector field comes from.
width - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D: Width of currently processed image.
width - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper: Width of reference image domain.
width - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Width of input label image.
width - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Width of the image.
width - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: Size of the image and the calculated gvf field in x-direction.
width - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
width - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform: Width of the given image.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D: Width of segmentation domain.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D: Width of segmentation domain.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents: Image width.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents: Image width.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation: Width of label images.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure: Width of label images.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter: Input image width.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE: Width of the input image and levelset function.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE: Width of the input image.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased: Width of the given image for the energy.
widthLengthTab - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D: Table with vessel widths and lengths to apply.
widths - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
widths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
window - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow: Main frame.
window - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow: Main frame.
window - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin: Main frame.
window - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
windowHeight - Static variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Height of the frame.
windowWidth - Static variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Width of the frame.
winSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack: Size of local sliding window.
workImage - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Internal image to work on.
workImgMaxVal - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder: Maximum intensity value in working image, i.e. after potential inversion of image intensity values.
workingImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle: Image on which to actually do the segmentation.
workingMatrix - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm: Local copy of matrix modified during calculations.
workVectorField - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D: Local vector field variable actually used during operator run.
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Write this contour set into XML file filename.xml Additionally, its processing history is written.
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Write this polygon set as xml into file filename.xml Additionally the processing history is written.
write(String, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Write this polygon set as xml into file filename If flag is set to true, the processing history is written, too.
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Write this region set to disk in XML format using MiToBo's xml-scheme MTBRegion2DSet.xsd
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag: Write this bag of region sets to disk in XML format using MiToBo's xml-scheme MTBRegion2DSetBag.xsd
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Write this set of 3D-regions to disk in XML format using MiToBo's xml-scheme MTBRegion3DSet.xsd
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerImageData
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerRegion2DSet
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerSegResultParticlesMultiChannel
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerTableModel
writeData(Object, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile
writeData(Object, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBImageDataIO
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBWrapperDataIOSwing
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtColorDataIOXmlbeans
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtPoint2dDataIOXmlbeans
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBDataIOFileXmlbeans
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBImageDataIOXmlbeans
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBTableModelDataIOXmlbeans
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBWrapperDataIOXmlbeans
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.RandomGeneratorDataIOXmlbeans
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOXmlbeans
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
writeGlobalAttributes(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
writeGraph(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
writeImagePlus(String, ImagePlus) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Write ImagePlus to disk
writeMTBImage(String, MTBImage) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB: Write an MTBImage to disk
writeMultiStates(Vector<MultiState<MotionModelID>>, String) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.MultiStateIO: Write a vector of MultiState objects to file in its xml-beans representation.
writeNodeLabels(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
writePartitions(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
WRITER_OPTIONS_APPROVED_PROPERTY - Static variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane: Property change when writer options are approved (i.e. when filechooser selection is approved)
writeRoiToFile(MTBRegion2D, String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter: Writes the given region to the specified file in csv format.
writeSubgraphs(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
WriteXML - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml: Writes markers of an image to file in XML format.
WriteXML(String) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.WriteXML: Creates a new instance of ODWriteXMLODD
writeXML(String, Vector<?>, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.WriteXML
wthImage - Variable in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement: White top-hat image.
wthMaskSize - Variable in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement

X

x - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
x - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
x - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Point coordinate at x-dimension.
x - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: x-coordinate of marker.
x - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.CoordInt3D
x - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
x - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
X - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber: 8- or 26 neighbors of the current pixel used to determine topological numbers represented as an 3x3x3 array center around the current pixel.
X_COMPONENT_INDEX - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
xc - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder.GraphNode: x-coordinate associated with the node.
xField - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel: Field for x-coordinate.
xFlow - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Vector field flow in x-direction.
xFlow - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: The flows of the field in x- and y-direction.
xLabel - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Label of the x-axis.
xLabel - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Label of the x-axis.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Maximal x-coordinate of the domain of this border set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Maximal x coordinate of the domain of this contour set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Maximal x coordinate of the domain of this polygon set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Maximal x coordinate of the domain of this region set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Maximal x coordinate of the domain of this region set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Maximal x coordinate of the domain of this region set.
xMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
xMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
xMean - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
xMeanSum - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Minimal x-coordinate of the domain of this border set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Minimal x coordinate of the domain of this contour set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Minimal x coordinate of the domain of this polygon set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Minimal x coordinate of the domain of this region set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Minimal x coordinate of the domain of this region set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Minimal x coordinate of the domain of this region set.
xMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
xMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
xml - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage: File description XML string if available
XMLBuffOut - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.WriteXML
XMLFileOut - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.WriteXML
XMLTypeConverter - Class in de.unihalle.informatik.MiToBo.tools: A class providing static methods to convert specific object to and from their corresponding xml-types provided by xml-beans.
XMLTypeConverter() - Constructor for class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
xMTBImg - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter: Result Image.
xOffset - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker: x-offset of the mask coordinate system.
xPos - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: y-position of the node in 2D image space.
xSize - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Size of input image in x dimension.
xThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: The Intensity/Brightness/Value threshold.
xThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: The Intensity/Brightness/Value threshold.
XylemDetector - Class in de.unihalle.informatik.MiToBo.apps.xylem: This operator implements xylem detection in RGB or HSX images.
XylemDetector() - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: Default Constructor.
xylemGrayedImage - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: The Xylem Cell microscope MTBImageByte grey level image.
XylemGrower - Class in de.unihalle.informatik.MiToBo.apps.xylem: This operators implements region growing for xylem segmentation.
XylemGrower() - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: Default Constructor.
XylemGrower(MTBImageByte, MTBImageByte, XylemGrower.GrowingMode) - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
XylemGrower.GrowingMode - Enum in de.unihalle.informatik.MiToBo.apps.xylem: The region growing modus.
XylemGrower.GrowingRegion2D - Class in de.unihalle.informatik.MiToBo.apps.xylem: This class is responsible for the growing of a single MTBRegion2D which is the result of the preprocessing steps.
XylemGrower.Neighbourhood - Enum in de.unihalle.informatik.MiToBo.apps.xylem: The kind of neighbourhood to inspect a pixel.
XylemGrower.SortMode - Enum in de.unihalle.informatik.MiToBo.apps.xylem: Sort Mode for different MTBRegion2D's.
xylemHsxImage - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: HS(X)-Color Channel Image.
xylemHsxImage - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower: HS(X)-Color Channel Image.
XylemInitialSegmentation - Class in de.unihalle.informatik.MiToBo.apps.xylem: Purpose of this operator is to make an initial segmentation of Xylem Cell Images.
XylemInitialSegmentation() - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation: Default constructor.
XylemInitialSegmentation(MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
xylemRegionsOverlay - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: Resulting regions from growing.
xylemRGBImage - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector: RGB-Color Channel Image.

Y

y - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
y - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
y - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Point coordinate at y-dimension.
y - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: y-coordinate of marker.
y - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.CoordInt3D
y - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
y - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
yc - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder.GraphNode: y-coordinate associated with the node.
yellow - Static variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer: Definition of yellow color.
yesnoOption - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin: Deprecated.

Labels to be used on buttons of Yes/No message boxes.
yField - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel: Field for y-coordinate.
yFlow - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D: Vector field flow in y-direction.
yFlow - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D: The flows of the field in x- and y-direction.
yLabel - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter: Label of the y-axis.
yLabel - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter: Label of the y-axis.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Maximal y-coordinate of the domain of this border set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Maximal y coordinate of the domain of this contour set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Maximal y coordinate of the domain of this polygon set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Maximal y coordinate of the domain of this region set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Maximal y coordinate of the domain of this region set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Maximal y coordinate of the domain of this region set.
yMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
yMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet: Minimal y-coordinate of the domain of this border set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet: Minimal y coordinate of the domain of this contour set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet: Minimal y coordinate of the domain of this polygon set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet: Minimal y coordinate of the domain of this region set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Minimal y coordinate of the domain of this region set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Minimal y coordinate of the domain of this region set.
yMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
yMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
yOffset - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker: y-offset of the mask coordinate system.
yPos - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData: y-position of the node in 2D image space.
ySize - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Size of input image in y dimension.

Z

z - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
z - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D: Point coordinate at z-dimension.
z - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker: z-coordinate of marker.
z - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.CoordInt3D
z - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
z - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
Z - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution: observations
Zadj - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency: adjacency votes matrix: which observations are associated (same track) and how many particles vote for these associations
zMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Maximal z coordinate of the domain of this region set.
zMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Maximal z coordinate of the domain of this region set.
zMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet: Minimal z coordinate of the domain of this region set.
zMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet: Minimal z coordinate of the domain of this region set.
zSize - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D: Size of input image in z dimension.
ztcCoords - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse: Optional coordinates for slices in ztc stack.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z