de.unihalle.informatik.MiToBo.apps.nuclei2D

Class NuclearParticleDetector2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              allowBatchMode=true,
              shortDescription="Detects nuclei and particles inside these nuclei.")
public class NuclearParticleDetector2D
extends MTBOperator

 
 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.

Author:

Danny Misiak

See Also:

NucleusDetector2D, ParticleDetectorUWT2D

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
protected Boolean	correctGamma
private String	fileName Name of input image file.
protected Boolean	filterImage
protected Double	gamma
private MTBImage	inputImage
private Integer	nucChannel
private NucleusDetector2D	nucDetector
private MTBImage	nucImage Part of the input image, representing the stained nuclei.
private MTBRegion2DSet	nucleiRegions
private Integer	partChannel
private ParticleDetectorUWT2D	partDetector
private MTBRegion2DSet	particleRegions
private MTBImage	partImage Part of the input image, representing the stained particles.
private MTBTableModel	resultTable
private int	sizeX Image width.
private int	sizeY Image height.
protected Boolean	swapNuclei

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
NuclearParticleDetector2D() Standard constructor.
NuclearParticleDetector2D(MTBImageByte _inputImage, Integer _nucChannel, Integer _partChannel, Boolean _correctGamma, Double _gamma, Boolean _filterImage, NucleusDetector2D _nucDetector, ParticleDetectorUWT2D _partDetector)

Method Summary

Modifier and Type	Method and Description
private void	createResultTable(Vector<Vector<Integer>> particleMatching) Create result table with statistics about nuclei and particles.
private void	createSwapResultTable() Create result table with statistics about nuclei and particles.
Boolean	getCorrectGamma() Get flag to use gamma correction.
String	getDocumentation()
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.
private Vector<Vector<Integer>>	matchParticles(MTBRegion2DSet tmpPartRegions) Match particle regions to nuclei regions.
protected void	operate()
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.
private void	useGammaCorrection() Callback routine to change parameters.
void	validateCustom() Custom validation of some input parameters.

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

inputImage

@Parameter(label="Input Image",
           required=true,
           direction=IN,
           description="Input image.",
           mode=STANDARD,
           dataIOOrder=0)
private transient MTBImage inputImage

nucChannel

@Parameter(label="Nuclei Channel",
           required=true,
           direction=IN,
           description="Channel number of nuclei stain.",
           mode=STANDARD,
           dataIOOrder=1)
private Integer nucChannel

partChannel

@Parameter(label="Particle Channel",
           required=true,
           direction=IN,
           description="Channel number of particle stain.",
           mode=STANDARD,
           dataIOOrder=2)
private Integer partChannel

correctGamma

@Parameter(label="Use Gamma Correction",
           required=true,
           direction=IN,
           description="Flag to use gamma correction.",
           mode=ADVANCED,
           callback="useGammaCorrection",
           paramModificationMode=MODIFIES_INTERFACE,
           dataIOOrder=3)
protected Boolean correctGamma

gamma

@Parameter(label="Gamma Value",
           required=true,
           direction=IN,
           description="Gamma correction value.",
           mode=ADVANCED,
           dataIOOrder=4)
protected Double gamma

filterImage

@Parameter(label="Use Gaussian Filter",
           required=true,
           direction=IN,
           description="Flag to use gaussian filter.",
           mode=ADVANCED,
           dataIOOrder=5)
protected Boolean filterImage

swapNuclei

@Parameter(label="Nuclei Intensity in Particle Channel",
           required=true,
           direction=IN,
           description="Flag to use nuclei intensity in particle channel.",
           mode=ADVANCED,
           dataIOOrder=6)
protected Boolean swapNuclei

nucDetector

@Parameter(label="Nucleus Detector",
           required=true,
           direction=IN,
           description="Detector for nuclei.",
           mode=ADVANCED,
           dataIOOrder=7)
private NucleusDetector2D nucDetector

partDetector

@Parameter(label="Particle Detector",
           required=true,
           direction=IN,
           description="Detector for particles.",
           mode=ADVANCED,
           dataIOOrder=8)
private ParticleDetectorUWT2D partDetector

nucleiRegions

@Parameter(label="Nuclei Regions",
           required=true,
           direction=OUT,
           description="Nuclei regions.")
private transient MTBRegion2DSet nucleiRegions

particleRegions

@Parameter(label="Particle Regions",
           required=false,
           direction=OUT,
           description="Particle regions.")
private transient MTBRegion2DSet particleRegions

resultTable

@Parameter(label="Result Table",
           required=true,
           direction=OUT,
           description="Particle statistics.")
private transient MTBTableModel resultTable

sizeX

private int sizeX

Image width.

sizeY

private int sizeY

Image height.

fileName

private String fileName

Name of input image file.

nucImage

private transient MTBImage nucImage

Part of the input image, representing the stained nuclei.

partImage

private transient MTBImage partImage

Part of the input image, representing the stained particles.

Constructor Detail

NuclearParticleDetector2D

public NuclearParticleDetector2D()
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Standard constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

NuclearParticleDetector2D

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

Parameters:

_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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Custom validation of some input parameters.

Overrides:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

useGammaCorrection

private void useGammaCorrection()

Callback routine to change parameters.

getInputImage

public MTBImage getInputImage()

Get input image.

setInputImage

public void setInputImage(MTBImageByte _inputImage)

Set input image.

getNucleiChannel

public Integer getNucleiChannel()

Get nuclei channel number.

setNucleiChannel

public void setNucleiChannel(Integer _nucChannel)

Set nuclei channel number.

getPartChannel

public Integer getPartChannel()

Get particle channel number.

setPartChannel

public void setPartChannel(Integer _partChannel)

Set particle channel number.

getCorrectGamma

public Boolean getCorrectGamma()

Get flag to use gamma correction.

setCorrectGamma

public void setCorrectGamma(Boolean _correctGamma)

Set flag to use gamma correction.

getGamma

public Double getGamma()

Get gamma correction value.

setGamma

public void setGamma(Double _gamma)

Set gamma correction value.

getFilterImage

public Boolean getFilterImage()

Get flag to use gaussian filter.

setFilterImage

public void setFilterImage(Boolean _filterImage)

Set flag to use gaussian filter.

getNucDetector

public NucleusDetector2D getNucDetector()

Get detector for nuclei.

setNucDetector

public void setNucDetector(NucleusDetector2D _nucDetector)

Set detector for nuclei.

getPartDetector

public ParticleDetectorUWT2D getPartDetector()

Get detector for particles.

setPartDetector

public void setPartDetector(ParticleDetectorUWT2D _partDetector)

Set detector for particles.

getNucleiRegions

public MTBRegion2DSet getNucleiRegions()

Get detected nuclei regions.

getParticleRegions

public MTBRegion2DSet getParticleRegions()

Get detected particle regions.

getResultTable

public MTBTableModel getResultTable()

Get particle statistics.

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

matchParticles

private Vector<Vector<Integer>> matchParticles(MTBRegion2DSet tmpPartRegions)

Match particle regions to nuclei regions.

Returns:

Indices of nuclei with corresponding particle indices.

createResultTable

private void createResultTable(Vector<Vector<Integer>> particleMatching)

Create result table with statistics about nuclei and particles.

createSwapResultTable

private void createSwapResultTable()

Create result table with statistics about nuclei and particles.

getDocumentation

public String getDocumentation()

Overrides:

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