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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.NuclearParticleDetector2D
@ALDAOperator(genericExecutionMode=ALL, level=APPLICATION, allowBatchMode=true) @ALDMetaInfo(export=MANDATORY) public class NuclearParticleDetector2D
This class detects nuclei and particles inside these nuclei and gives some statistics about particles, like particle number per nuclei, particle size, sum of intensities, etc. Nuclei are detected via the NucleusDetector2D by using the Niblack thresholding. As post-process the nuclei channel is gamma corrected and filter with a small gaussian, due to uneven illumination of the nuclei in the images. This may depends on the input image data and can be switched off separately. Particles are detected via the ParticleDetectorUWT2D.
NucleusDetector2D
,
ParticleDetectorUWT2D
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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protected Boolean |
correctGamma
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protected Boolean |
filterImage
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protected Double |
gamma
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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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NuclearParticleDetector2D()
Standard constructor. |
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NuclearParticleDetector2D(MTBImageByte _inputImage,
Integer _nucChannel,
Integer _partChannel,
Boolean _correctGamma,
Double _gamma,
Boolean _filterImage,
NucleusDetector2D _nucDetector,
ParticleDetectorUWT2D _partDetector)
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Method Summary | |
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Boolean |
getCorrectGamma()
Get flag to use gamma correction. |
Boolean |
getFilterImage()
Get flag to use gaussian filter. |
Double |
getGamma()
Get gamma correction value. |
MTBImage |
getInputImage()
Get input image. |
NucleusDetector2D |
getNucDetector()
Get detector for nuclei. |
Integer |
getNucleiChannel()
Get nuclei channel number. |
MTBRegion2DSet |
getNucleiRegions()
Get detected nuclei regions. |
Integer |
getPartChannel()
Get particle channel number. |
ParticleDetectorUWT2D |
getPartDetector()
Get detector for particles. |
MTBRegion2DSet |
getParticleRegions()
Get detected particle regions. |
MTBTableModel |
getResultTable()
Get particle statistics. |
protected void |
operate()
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void |
setCorrectGamma(Boolean _correctGamma)
Set flag to use gamma correction. |
void |
setFilterImage(Boolean _filterImage)
Set flag to use gaussian filter. |
void |
setGamma(Double _gamma)
Set gamma correction value. |
void |
setInputImage(MTBImageByte _inputImage)
Set input image. |
void |
setNucDetector(NucleusDetector2D _nucDetector)
Set detector for nuclei. |
void |
setNucleiChannel(Integer _nucChannel)
Set nuclei channel number. |
void |
setPartChannel(Integer _partChannel)
Set particle channel number. |
void |
setPartDetector(ParticleDetectorUWT2D _partDetector)
Set detector for particles. |
void |
validateCustom()
Custom validation of some input parameters. |
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 |
Field Detail |
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@Parameter(label="Use Gamma Correction", required=true, direction=IN, description="Flag to use gamma correction.", mode=ADVANCED, dataIOOrder=3) protected Boolean correctGamma
@Parameter(label="Gamma Value", required=true, direction=IN, description="Gamma correction value.", mode=ADVANCED, dataIOOrder=4) protected Double gamma
@Parameter(label="Use Gaussian Filter", required=true, direction=IN, description="Flag to use gaussian filter.", mode=ADVANCED, dataIOOrder=5) protected Boolean filterImage
Constructor Detail |
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public NuclearParticleDetector2D() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public NuclearParticleDetector2D(MTBImageByte _inputImage, Integer _nucChannel, Integer _partChannel, Boolean _correctGamma, Double _gamma, Boolean _filterImage, NucleusDetector2D _nucDetector, ParticleDetectorUWT2D _partDetector) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
_inputImage
- input image_nucChannel
- channel number of nuclei stain_partChannel
- channel number of particle stain_correctGamma
- flag to use gamma correction_gamma
- gamma correction value_filterImage
- flag to use gaussian filter_nucDetector
- detector for nuclei_partDetector
- detector for particles
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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public void validateCustom() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
validateCustom
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public MTBImage getInputImage()
public void setInputImage(MTBImageByte _inputImage)
public Integer getNucleiChannel()
public void setNucleiChannel(Integer _nucChannel)
public Integer getPartChannel()
public void setPartChannel(Integer _partChannel)
public Boolean getCorrectGamma()
public void setCorrectGamma(Boolean _correctGamma)
public Double getGamma()
public void setGamma(Double _gamma)
public Boolean getFilterImage()
public void setFilterImage(Boolean _filterImage)
public NucleusDetector2D getNucDetector()
public void setNucDetector(NucleusDetector2D _nucDetector)
public ParticleDetectorUWT2D getPartDetector()
public void setPartDetector(ParticleDetectorUWT2D _partDetector)
public MTBRegion2DSet getNucleiRegions()
public MTBRegion2DSet getParticleRegions()
public MTBTableModel getResultTable()
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
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