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java.lang.Objectde.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
@ALDAOperator(genericExecutionMode=ALL, level=STANDARD) public class FluorescentCellSegmenter
This operator is for segmenting images or image sequences containing fluorescently labeled cells
Nested Class Summary |
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Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode |
Field Summary |
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Fields inherited from class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter |
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channel, inImg, minSeedSize, resultImg, seedImg, sizeC, sizeT, sizeX, sizeY, sizeZ |
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider |
Constructor Summary | |
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FluorescentCellSegmenter()
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FluorescentCellSegmenter(MTBImage inImg)
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Method Summary | |
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MTBImage |
getResultImage()
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protected MTBImage |
getSeedPoints(MTBImage frame)
coarse segmentation of input frame to localize cells |
protected MTBImage |
preprocess(MTBImage frame)
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protected MTBImage |
segment(MTBImage frame,
MTBImage seedFrame)
segment cells in a single frame of the input image |
void |
setGamma(double gamma)
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void |
setMaxIteration(int maxIter)
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void |
setMedianMaskSize(int size)
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Methods inherited from class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter |
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operate, setChannel, setMinSeedSize, setSeedPointImage, validateCustom, verbosePrintln |
Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator |
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readResolve |
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public FluorescentCellSegmenter() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public FluorescentCellSegmenter(MTBImage inImg) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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protected MTBImage segment(MTBImage frame, MTBImage seedFrame) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
CellSegmenter
segment
in class CellSegmenter
frame
- input frame
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
protected MTBImage getSeedPoints(MTBImage frame) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
getSeedPoints
in class CellSegmenter
frame
-
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
protected MTBImage preprocess(MTBImage frame) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
preprocess
in class CellSegmenter
frame
-
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
public void setMedianMaskSize(int size)
size
- public void setMaxIteration(int maxIter)
maxIter
- public void setGamma(double gamma)
gamma
- public MTBImage getResultImage()
getResultImage
in class CellSegmenter
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