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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
@ALDAOperator(genericExecutionMode=ALL) public class NucleusDetector2D
Operator for segmenting cell nuclei in 2D images.
Nested Class Summary | |
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static class |
NucleusDetector2D.NuclDetectMode
Available modes for nuclei segmentation in 2D images. |
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.Alida.operator.ALDOperator |
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completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider |
Constructor Summary | |
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NucleusDetector2D()
Default constructor. |
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NucleusDetector2D(MTBImage img,
NucleusDetector2D.NuclDetectMode opmode,
ImgThreshNiblack niblackOp,
boolean doMorph,
int msize,
int minSize,
boolean fillHoles)
Constructor. |
Method Summary | |
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protected MTBImageByte |
detectWithLocalContrastEnhancement()
Detect nuclei by first improving image contrast. |
protected MTBImageByte |
detectWithNiblack()
Detects nuclei based on Niblack thresholding. |
protected MTBImageByte |
detectWithOtsu_erodedilate()
Detects nuclei based on Otsu thresholding and a combination of erosion/ dilation. |
protected MTBImageByte |
detectWithOtsu_openclose()
Detects nuclei based on Otsu thresholding and a combination of opening and closing. |
SegResult_Nuclei |
getResultData()
Get the result data, i.e. mask and related quantitative data. |
MTBImage |
getResultImage()
Get the result label image. |
protected void |
operate()
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void |
setInputImage(MTBImage img)
Specify input image. |
void |
setMeasureUnits(SegResultEnums.MeasureUnit mu)
Specify units in which to measure areas. |
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, validateCustom, 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 NucleusDetector2D() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public NucleusDetector2D(MTBImage img, NucleusDetector2D.NuclDetectMode opmode, ImgThreshNiblack niblackOp, boolean doMorph, int msize, int minSize, boolean fillHoles) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
img
- Image to be processed.opmode
- Detection mode.niblackOp
- Optional Niblack operator for mode 'NIBLACK'.doMorph
- Flag to enable/disable morphological processing.msize
- Size of structuring element in pre-/postprocessing.minSize
- Minimum size of valid nuclei.fillHoles
- Flag to enable/disable hole filling.
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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public void setInputImage(MTBImage img)
public void setMeasureUnits(SegResultEnums.MeasureUnit mu)
public MTBImage getResultImage()
public SegResult_Nuclei getResultData()
protected void operate() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
operate
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
protected MTBImageByte detectWithOtsu_openclose() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
protected MTBImageByte detectWithOtsu_erodedilate() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
This routine has been developed by Jochen Luechtrath for nuclei/cytoplasm segmentation.
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
protected MTBImageByte detectWithNiblack() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
protected MTBImageByte detectWithLocalContrastEnhancement() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
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