de.unihalle.informatik.MiToBo.apps.singleCellTracking2D

Class CellMigrationAnalyzer

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.MiToBo.core.operator.MTBOperator

de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              allowBatchMode=false,
              shortDescription="Operator for segmenting, tracking and analyzing 2D image sequences of fluorescently labeled cells.")
public class CellMigrationAnalyzer
extends MTBOperator

Operator for segmenting, tracking and analyzing 2D image sequences of fluorescently labeled cells

Author:

glass

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 Boolean	analyzeIntensities
private Boolean	analyzeShapes
private Boolean	analyzeTrajectories
private Double	avgFactor
private Double	deltaT
private Double	deltaX
private Double	deltaY
private Integer	detectionChannel
private Double	gamma
private Boolean	include
private MTBImage	inImg
private String	intReport
private MTBImage	labelResult
private Integer	maskChannel
private Double	maxAreaChange
private Double	maxDist
private Integer	maxIter
private Integer	minArea
private Integer	minSeedSize
private Integer	minTrackLength
private Boolean	removeBorderObjects
private Boolean	removeExcluded
private MTBImage	segmentationResult
private String	shapeReport
private Boolean	showOverlayImage
private Boolean	showTrajectoryMap
private Integer	sigma
private String	trackReport
private String	unitT
private String	unitXY
private Boolean	useAutoDistance
private Boolean	useMask

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
CellMigrationAnalyzer()
CellMigrationAnalyzer(MTBImage img)

Method Summary

Modifier and Type	Method and Description
private void	getCalibration()
String	getDocumentation()
protected void	operate()
private void	showMaskChannelTextbox()
private void	showMaxDistTextbox()

Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator

readResolve

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

addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, 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, 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

inImg

@Parameter(label="input image",
           required=true,
           direction=IN,
           supplemental=false,
           description="input image",
           dataIOOrder=0,
           callback="getCalibration",
           paramModificationMode=MODIFIES_INTERFACE)
private transient MTBImage inImg

detectionChannel

@Parameter(label="detection channel",
           required=true,
           direction=IN,
           supplemental=false,
           description="detection channel",
           dataIOOrder=1)
private Integer detectionChannel

minSeedSize

@Parameter(label="minimum seed size",
           required=false,
           direction=IN,
           supplemental=false,
           description="minimum size for seeds to be not discarded",
           dataIOOrder=2,
           mode=ADVANCED)
private Integer minSeedSize

sigma

@Parameter(label="\u03c3",
           required=false,
           direction=IN,
           supplemental=false,
           description="standard deviation of Gaussian filter mask",
           dataIOOrder=3)
private Integer sigma

gamma

@Parameter(label=" \u03b3",
           required=false,
           direction=IN,
           supplemental=false,
           description="value for \u03b3-correction for emphasizing cells",
           dataIOOrder=4)
private Double gamma

maxIter

@Parameter(label="maximum number of iterations",
           required=false,
           direction=IN,
           supplemental=false,
           description="maximum number of iterations for level set evolution",
           dataIOOrder=5,
           mode=ADVANCED)
private Integer maxIter

useMask

@Parameter(label="use mask channel",
           required=false,
           direction=IN,
           supplemental=false,
           description="use mask channel",
           dataIOOrder=6,
           mode=ADVANCED,
           callback="showMaskChannelTextbox",
           paramModificationMode=MODIFIES_INTERFACE)
private Boolean useMask

maskChannel

@Parameter(label="mask channel",
           required=false,
           direction=IN,
           supplemental=false,
           description="mask channel",
           dataIOOrder=7,
           mode=ADVANCED)
private Integer maskChannel

include

@Parameter(label="include bright objects from mask",
           required=false,
           direction=IN,
           supplemental=false,
           description="include tracks that have sufficient signals in mask image (otherwise these tracks are excluded)",
           dataIOOrder=8,
           mode=ADVANCED)
private Boolean include

avgFactor

@Parameter(label="average factor",
           required=false,
           direction=IN,
           supplemental=false,
           description="object\'s mean intensity must be at least mean image intensity multiplied with this factor to be included/ excluded",
           dataIOOrder=9,
           mode=ADVANCED)
private Double avgFactor

removeBorderObjects

@Parameter(label="remove border touching objects",
           required=false,
           direction=IN,
           supplemental=false,
           description="should border touching objects be removed",
           dataIOOrder=10,
           mode=ADVANCED)
private Boolean removeBorderObjects

minArea

@Parameter(label="minimum area (pixels)",
           required=false,
           direction=IN,
           supplemental=false,
           description="minimum area (number of pixels) an object should have",
           dataIOOrder=11)
private Integer minArea

useAutoDistance

@Parameter(label="determine gating distance automatically",
           required=false,
           direction=IN,
           supplemental=false,
           description="determine gating distance automatically",
           dataIOOrder=12,
           mode=ADVANCED,
           callback="showMaxDistTextbox",
           paramModificationMode=MODIFIES_INTERFACE)
private Boolean useAutoDistance

maxDist

@Parameter(label="maximum distance (pixels)",
           required=false,
           direction=IN,
           supplemental=false,
           description="maximum distance for two objects to be assigned to each other",
           dataIOOrder=13,
           mode=ADVANCED)
private Double maxDist

maxAreaChange

@Parameter(label="maximum area change",
           required=false,
           direction=IN,
           supplemental=false,
           description="maximum change in area (fraction) for two objects to be assigned to each other",
           dataIOOrder=14)
private Double maxAreaChange

deltaX

@Parameter(label="pixel length, x-direction",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in x-direction",
           dataIOOrder=15)
private Double deltaX

deltaY

@Parameter(label="pixel length, y-direction",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in y-direction",
           dataIOOrder=16)
private Double deltaY

unitXY

@Parameter(label="unit space",
           required=false,
           direction=IN,
           supplemental=false,
           description="unit x/y",
           dataIOOrder=17)
private String unitXY

deltaT

@Parameter(label="time between frames",
           required=false,
           direction=IN,
           supplemental=false,
           description="time between frames",
           dataIOOrder=18)
private Double deltaT

unitT

@Parameter(label="unit time",
           required=false,
           direction=IN,
           supplemental=false,
           description="unit time",
           dataIOOrder=19)
private String unitT

minTrackLength

@Parameter(label="minimum track length",
           required=false,
           direction=IN,
           supplemental=false,
           description="minimum track length to be considered",
           dataIOOrder=20)
private Integer minTrackLength

analyzeTrajectories

@Parameter(label="analyze trajectories",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the objects\' trajectories be analyzed",
           dataIOOrder=21)
private Boolean analyzeTrajectories

analyzeShapes

@Parameter(label="analyze shapes",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the objects\' shapes be analyzed",
           dataIOOrder=22)
private Boolean analyzeShapes

analyzeIntensities

@Parameter(label="analyze intensities",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the objects\' intensities be analyzed",
           dataIOOrder=23)
private Boolean analyzeIntensities

showTrajectoryMap

@Parameter(label="show trajectory map",
           required=false,
           direction=IN,
           supplemental=false,
           description="should a 2D map of the extracted trajectories be shown",
           dataIOOrder=24)
private Boolean showTrajectoryMap

showOverlayImage

@Parameter(label="show overlay image",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the extracted trajectories be shown overlayed on the cells",
           dataIOOrder=25)
private Boolean showOverlayImage

removeExcluded

@Parameter(label="remove excluded objects",
           required=false,
           direction=IN,
           supplemental=false,
           description="should objects that weren\'t analyzed be removed from the label image",
           dataIOOrder=26)
private Boolean removeExcluded

segmentationResult

private transient MTBImage segmentationResult

labelResult

@Parameter(label="label result",
           required=true,
           direction=OUT,
           supplemental=false,
           description="resulting label image")
private transient MTBImage labelResult

trackReport

@Parameter(label="track report",
           required=true,
           direction=OUT,
           supplemental=false,
           description="track report")
private String trackReport

shapeReport

@Parameter(label="shape report",
           required=true,
           direction=OUT,
           supplemental=false,
           description="shape report")
private String shapeReport

intReport

@Parameter(label="intensity report",
           required=true,
           direction=OUT,
           supplemental=false,
           description="intensity report")
private String intReport

Constructor Detail

CellMigrationAnalyzer

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

CellMigrationAnalyzer

public CellMigrationAnalyzer(MTBImage img)
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

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

getCalibration

private void getCalibration()

showMaskChannelTextbox

private void showMaskChannelTextbox()

showMaxDistTextbox

private void showMaxDistTextbox()

getDocumentation

public String getDocumentation()

Overrides:

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