de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators

Class CellCounterDetectOperatorStromules

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperatorCollectionElement

de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator

de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener, loci.common.StatusListener, loci.common.StatusReporter

@ALDAOperator(genericExecutionMode=NONE)
 @ALDDerivedClass
public class CellCounterDetectOperatorStromules
extends CellCounterDetectOperator

Detector wrapper for detection of stromules from given plastid regions.

This wrapper makes the stromule detector functionality of the StromulesDetector2D accessible from within the MTBCellCounter plugin - a plugin for semi-automatic counting of small, mainly spot-like structures in microscopy images.

For further details on the plugin and the methodology of the detector refer to

• B. Möller and M. Schattat, Quantification of Stromule Frequencies in Microscope Images of Plastids combining Ridge Detection and Geometric Criteria,
  in Proc. of 6th Int. Conf. on Bioimaging (BIOIMAGING '19), Prague, Czech Republic, February 2019.
• L. Franke, B. Storbeck, J. L. Erickson, D. Rödel, D. Schröter, B. Möller, and M. H. Schattat, The 'MTB Cell Counter' a versatile tool for the semi-automated quantification of sub-cellular phenotypes in fluorescence microscopy images. A case study on plastids, nuclei and peroxisomes, in Journal of Endocytobiosis and Cell Research, 26:31-42, 2015.

Author:

Birgit Moeller

See Also:

StegerRidgeDetection2DWrapper, StromulesDetector2D

Nested Class Summary

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
private double	ellipseDistThresh Maximal distance between contact points along ellipse contour.
private static String	opIdentifier Identifier for outputs in verbose mode.
private int	plastidMarkerType Type of plastid markers.
protected boolean	showAdditionalResults Show additional result images.
protected double	stromuliAngleThreshold Stromuli orientation angle criterion.
private StromulesDetector2D	stromuliOp Operator for stromuli detection.
protected boolean	useAngleCriterion Enable/disable angle criterion.
protected boolean	useEllipseDistThreshold Enable/disable ellipse distance threshold.
protected boolean	useMultiIntersectionCheck Enable/disable line multi-intersection check.

Fields inherited from class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator

detectResults, detectZSlice, highQualityData, inputImage, m_statusListeners, markerVects

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
CellCounterDetectOperatorStromules() Constructor.

Method Summary

Modifier and Type	Method and Description
String	getShortName() Get common short name of operator for GUI.
String	getUniqueClassIdentifier()
protected void	operate()

Methods inherited from class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator

addStatusListener, getDetectionResults, notifyListeners, removeStatusListener, setHighQualityData, setInputImage, setMarkerVectors, setSliceZid, statusUpdated

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getDocumentation, getHidingMode, getInactiveParameterNames, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterDescriptorUnconditioned, getParameterNames, getParameterUnconditioned, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, hasInOutParameters, hasParameter, isAnnotatedParameter, isConfigured, print, print, print, printInterface, printInterface, readHistory, readResolve, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, removeParameter, runOp, runOp, runOp, setConstructionMode, setConstructionMode, setConstructionMode, setHidingMode, setName, setParameter, setParameterUnconditioned, setVerbose, toStringVerbose, unconfiguredItems, validate, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

opIdentifier

private static final String opIdentifier

Identifier for outputs in verbose mode.

See Also:

Constant Field Values

plastidMarkerType

@Parameter(label="Plastid Marker Type",
           required=true,
           dataIOOrder=1,
           direction=IN,
           description="Plastid marker type.")
private int plastidMarkerType

Type of plastid markers.

useMultiIntersectionCheck

@Parameter(label="Apply line multi-intersection check?",
           required=true,
           dataIOOrder=11,
           direction=IN,
           mode=STANDARD,
           description="Checks if a potential stromuli line intersects a region at least twice, then it might be a reflection")
protected boolean useMultiIntersectionCheck

Enable/disable line multi-intersection check.

useEllipseDistThreshold

@Parameter(label="Apply ellipse distance threshold?",
           required=true,
           dataIOOrder=12,
           direction=IN,
           mode=STANDARD,
           description="Use Ellipse distance threshold.")
protected boolean useEllipseDistThreshold

Enable/disable ellipse distance threshold.

ellipseDistThresh

@Parameter(label="Ellipse distance threshold",
           required=true,
           dataIOOrder=13,
           direction=IN,
           description="Ellipse distance.")
private double ellipseDistThresh

Maximal distance between contact points along ellipse contour.

useAngleCriterion

@Parameter(label="Apply angle criterion?",
           required=true,
           dataIOOrder=15,
           direction=IN,
           mode=STANDARD,
           description="Apply stromuli angle criterion.")
protected boolean useAngleCriterion

Enable/disable angle criterion.

stromuliAngleThreshold

@Parameter(label="Stromuli angle threshold",
           required=true,
           dataIOOrder=16,
           direction=IN,
           mode=STANDARD,
           description="Stromuli-tangent angle threshold (in degrees).")
protected double stromuliAngleThreshold

Stromuli orientation angle criterion.

showAdditionalResults

@Parameter(label="Show additional intermediate results?",
           dataIOOrder=0,
           supplemental=true,
           direction=IN,
           mode=STANDARD,
           description="Enables display of additional result images.")
protected boolean showAdditionalResults

Show additional result images.

stromuliOp

private StromulesDetector2D stromuliOp

Operator for stromuli detection.

Constructor Detail

CellCounterDetectOperatorStromules

public CellCounterDetectOperatorStromules()
                                   throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of initialization error.

Method Detail

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Specified by:

operate in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getShortName

public String getShortName()

Description copied from class: CellCounterDetectOperator

Get common short name of operator for GUI.

Specified by:

getShortName in class CellCounterDetectOperator

Returns:

Name of operator.

getUniqueClassIdentifier

public String getUniqueClassIdentifier()

Specified by:

getUniqueClassIdentifier in class de.unihalle.informatik.Alida.operator.ALDOperatorCollectionElement