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

java.lang.Object
  extended by de.unihalle.informatik.Alida.operator.ALDOperator
      extended by de.unihalle.informatik.MiToBo.core.operator.MTBOperator
          extended by de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
              extended by 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)
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
 
Field Summary
 
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
FluorescentCellSegmenter()
           
FluorescentCellSegmenter(MTBImage inImg)
           
 
Method Summary
 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 setMedianMaskSize(int size)
           
 
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, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getHidingMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, runOp, runOp, runOp, setConstructionMode, setHidingMode, setName, setParameter, 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
 

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

setMedianMaskSize

public void setMedianMaskSize(int size)
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


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