de.unihalle.informatik.MiToBo.apps.nuclei2D

Class NucleusDetector2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              shortDescription="Operator for segmenting cell nuclei in 2D images.")
public class NucleusDetector2D
extends MTBOperator

Operator for segmenting cell nuclei in 2D images.

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	NucleusDetector2D.NuclDetectMode Available modes for nuclei segmentation in 2D images.

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
private LocallyAdaptiveContrastEnhancement	contrastEnhancer
private boolean	doFillHoles Flag to enable hole filling.
private boolean	doMorphOps Flag to enable/disable morphological pre-/postprocessing.
private boolean	doNucleiSeparation Flag to enable separation of merged nuclei regions.
private MTBImageShort	inImg Reference to original image, for internal use only
private MTBImage	inImgOrig Input image to process.
private SegResultEnums.MeasureUnit	measureUnits Units to be used for measurements.
private int	minNucleusSize Minimal size of valid nuclei regions.
private int	morphMaskSize Mask size to be used in morphological pre-/postprocessing.
private ImgThreshNiblack	niblackOperator Niblack operator, required if mode is 'NIBLACK'.
private NucleusSeparator2D	nucleusSepOp Operator to be applied for nuclei separation.
private NucleusDetector2D.NuclDetectMode	opMode Detection mode.
private SegResult_Nuclei	resultData Result data object containing quantitative data and label images.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
NucleusDetector2D() Default constructor.
NucleusDetector2D(MTBImage img, NucleusDetector2D.NuclDetectMode opmode, ImgThreshNiblack niblackOp, boolean doMorph, int msize, int minSize, boolean fillHoles) Constructor.

Method Summary

Modifier and Type	Method and Description
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.
String	getDocumentation()
SegResult_Nuclei	getResultData() Get the result data, i.e. mask and related quantitative data.
MTBImage	getResultImage() Get the result label image.
protected void	operate()
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

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, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

inImgOrig

@Parameter(label="Input image",
           required=true,
           direction=IN,
           description="Input image.",
           dataIOOrder=-10)
private transient MTBImage inImgOrig

Input image to process.

opMode

@Parameter(label="Operator mode",
           required=true,
           dataIOOrder=-9,
           direction=IN,
           description="Operator detection mode.")
private NucleusDetector2D.NuclDetectMode opMode

Detection mode.

niblackOperator

@Parameter(label="Niblack operator",
           required=false,
           dataIOOrder=-1,
           direction=IN,
           description="Niblack thresholder.")
private ImgThreshNiblack niblackOperator

Niblack operator, required if mode is 'NIBLACK'.

doMorphOps

@Parameter(label="Apply morphological operations",
           required=false,
           direction=IN,
           description="Apply morphological operations.",
           dataIOOrder=-9)
private boolean doMorphOps

Flag to enable/disable morphological pre-/postprocessing.

Flag is only active if mode is not 'NIBLACK'.

morphMaskSize

@Parameter(label="Masksize",
           required=false,
           dataIOOrder=-8,
           direction=IN,
           description="Structuring element size.")
private int morphMaskSize

Mask size to be used in morphological pre-/postprocessing.

minNucleusSize

@Parameter(label="Min. nuclei size",
           required=false,
           dataIOOrder=-11,
           direction=IN,
           description="Minimum size of valid nuclei.")
private int minNucleusSize

Minimal size of valid nuclei regions.

doFillHoles

@Parameter(label="Fill holes",
           required=false,
           dataIOOrder=-6,
           direction=IN,
           description="Fill holes in regions.")
private boolean doFillHoles

Flag to enable hole filling.

contrastEnhancer

@Parameter(label="Operator for local contrast improvement",
           required=false,
           dataIOOrder=1,
           direction=IN,
           description="Applied in mode CONTRAST_ANALYSIS.")
private LocallyAdaptiveContrastEnhancement contrastEnhancer

doNucleiSeparation

@Parameter(label="Try Nuclei Separation",
           required=false,
           dataIOOrder=2,
           direction=IN,
           description="Apply nuclei separator to split merged regions.")
private boolean doNucleiSeparation

Flag to enable separation of merged nuclei regions.

nucleusSepOp

@Parameter(label="Nuclei Separator",
           required=false,
           dataIOOrder=4,
           direction=IN,
           description="Operator for nuclei region splitting.")
private NucleusSeparator2D nucleusSepOp

Operator to be applied for nuclei separation.

measureUnits

@Parameter(label="Units",
           required=false,
           mode=ADVANCED,
           direction=IN,
           dataIOOrder=100,
           description="Units for area measurements.")
private SegResultEnums.MeasureUnit measureUnits

Units to be used for measurements.

resultData

@Parameter(label="Result statistics",
           direction=OUT,
           description="Quantitative result data.")
private transient SegResult_Nuclei resultData

Result data object containing quantitative data and label images.

inImg

private transient MTBImageShort inImg

Reference to original image, for internal use only

Constructor Detail

NucleusDetector2D

public NucleusDetector2D()
                  throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

NucleusDetector2D

public NucleusDetector2D(MTBImage img,
                         NucleusDetector2D.NuclDetectMode opmode,
                         ImgThreshNiblack niblackOp,
                         boolean doMorph,
                         int msize,
                         int minSize,
                         boolean fillHoles)
                  throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor.

Parameters:

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.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

setInputImage

public void setInputImage(MTBImage img)

Specify input image.

setMeasureUnits

public void setMeasureUnits(SegResultEnums.MeasureUnit mu)

Specify units in which to measure areas.

getResultImage

public MTBImage getResultImage()

Get the result label image.

Returns:

Reference to result label image, might be null.

getResultData

public SegResult_Nuclei getResultData()

Get the result data, i.e. mask and related quantitative data.

Returns:

Result data object.

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

detectWithOtsu_openclose

protected MTBImageByte detectWithOtsu_openclose()
                                         throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Detects nuclei based on Otsu thresholding and a combination of opening and closing.

Returns:

Label image with detected nuclei.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

detectWithOtsu_erodedilate

protected MTBImageByte detectWithOtsu_erodedilate()
                                           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                  de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Detects nuclei based on Otsu thresholding and a combination of erosion/ dilation.

This routine has been developed by Jochen Luechtrath for nuclei/cytoplasm segmentation.

Returns:

Label image with detected nuclei.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

detectWithNiblack

protected MTBImageByte detectWithNiblack()
                                  throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                         de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Detects nuclei based on Niblack thresholding.

Returns:

Label image with detected nuclei.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

detectWithLocalContrastEnhancement

protected MTBImageByte detectWithLocalContrastEnhancement()
                                                   throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                          de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Detect nuclei by first improving image contrast.

Returns:

Label image with detected nuclei.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getDocumentation

public String getDocumentation()

Overrides:

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