de.unihalle.informatik.MiToBo.apps.singleCellTracking2D

Class FluorescentCellSegmenter

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter

de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=STANDARD,
              shortDescription="Segments images or image sequences containing fluorescently labeled cells.")
public class FluorescentCellSegmenter
extends CellSegmenter

This operator is for segmenting images or image sequences containing 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 Double	gamma
private Integer	maxIter
private Integer	sigma

Fields inherited from class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter

channel, inImg, minSeedSize, resultImg, seedImg, sizeC, sizeT, sizeX, sizeY, sizeZ

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
FluorescentCellSegmenter()
FluorescentCellSegmenter(MTBImage inImg)

Method Summary

Modifier and Type	Method and Description
String	getDocumentation()
MTBImage	getResultImage()
protected MTBImage	getSeedPoints(MTBImage frame) coarse segmentation of input frame to localize cells
protected MTBImage	preprocess(MTBImage frame)
protected MTBImage	segment(MTBImage frame, MTBImage seedFrame) segment cells in a single frame of the input image
void	setGamma(double gamma)
void	setMaxIteration(int maxIter)
void	setSigma(int sigma)

Methods inherited from class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter

operate, setChannel, setMinSeedSize, setSeedPointImage, validateCustom, verbosePrintln

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, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

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

Field Detail

sigma

@Parameter(label="\u03c3",
           required=false,
           direction=IN,
           supplemental=false,
           description="standard deviation of Gaussian filter mask",
           dataIOOrder=1)
private Integer sigma

maxIter

@Parameter(label="maximum number of iterations",
           required=false,
           direction=IN,
           supplemental=false,
           description="maximum number of iterations for level set evolution",
           mode=ADVANCED,
           dataIOOrder=2)
private Integer maxIter

gamma

@Parameter(label=" \u03b3",
           required=false,
           direction=IN,
           supplemental=false,
           description="value for \u03b3-correction for emphasizing cells",
           mode=STANDARD,
           dataIOOrder=3)
private Double gamma

Constructor Detail

FluorescentCellSegmenter

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

FluorescentCellSegmenter

public FluorescentCellSegmenter(MTBImage inImg)
                         throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

segment

protected MTBImage segment(MTBImage frame,
                           MTBImage seedFrame)
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                           de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Description copied from class: CellSegmenter

segment cells in a single frame of the input image

Specified by:

segment in class CellSegmenter

Parameters:

frame - input frame

Returns:

segmented frame

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getSeedPoints

protected MTBImage getSeedPoints(MTBImage frame)
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                 de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

coarse segmentation of input frame to localize cells

Specified by:

getSeedPoints in class CellSegmenter

Parameters:

frame -

Returns:

image containing seed points for the given frame

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

preprocess

protected MTBImage preprocess(MTBImage frame)
                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                              de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Specified by:

preprocess in class CellSegmenter

Parameters:

frame -

Returns:

preprocessed frame

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

setSigma

public void setSigma(int sigma)

Parameters:

size -

setMaxIteration

public void setMaxIteration(int maxIter)

Parameters:

maxIter -

setGamma

public void setGamma(double gamma)

Parameters:

gamma -

getResultImage

public MTBImage getResultImage()

Overrides:

getResultImage in class CellSegmenter

Returns:

segmentation result

getDocumentation

public String getDocumentation()

Overrides:

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