de.unihalle.informatik.MiToBo.apps.cells2D

Class Mica2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperatorControllable

de.unihalle.informatik.MiToBo.core.operator.MTBOperatorControllable

de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDConfigurationEventListener, de.unihalle.informatik.Alida.operator.events.ALDConfigurationEventReporter, de.unihalle.informatik.Alida.operator.events.ALDControlEventListener, de.unihalle.informatik.Alida.operator.events.ALDControlEventReporter, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              shortDescription="Operator for integrated cell image analysis.")
public class Mica2D
extends MTBOperatorControllable

Operator for integrated cell image analysis.

Given a multi-channel input image this operator detects nuclei, particles and the cell boundary and integrates all results to complete cell statistics.

Author:

moeller

Nested Class Summary

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable

de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorControlStatus, de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorControlStatusHandle, de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorExecutionStatus

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 int	cellChannel Channel for cell boundary detection.
private int[]	channelsToCopy Set of image channels to copy into result stack.
private CytoplasmAnalyzer2D	cytoDetector Cytoplasma detection operator.
private boolean	doGauss Preprocess cytoplasm channel by Gaussian smoothing.
private boolean	excludeParticlesInNuclei Flag to ignore particle in nuclei regions.
private double	gaussSigma Sigma for Gaussian smoothing.
private boolean	imagesAsMasks If flag is true, only masks are copied to result stack.
private MTBImage	inImg Multi-channel input image.
private int	nucleiChannel Nuclei channel.
private MTBPolygon2DSet	nucleiContours (Optional) initial snake contours for nuclei.
private NucleusDetector2D	nucleiDetector Operator for nucleus detection/separation.
private MultiChannelParticleAnalyzer2D	particleDetector Particle detector.
private boolean	prepareFinalResultStack Flag for preparing final result image(s) stack.
private SegResult_Complete	resultData Result data object.
private SegResult_Cytoplasm	resultDataCells Local container for cell cytoplasm segmentation result.
private Vector<MTBImage>	resultImages Local container for set of segmentation result and channel copy images.
private Mica2DTableModel	resultStats Result data object.
private de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	saveIntermediateResultPath Path where to save intermediate results.
private boolean	saveIntermediateResults Flag for saving intermediate results to a specified directory.
private boolean	showIntermediateResults Flag for showing intermediate results.
private SegResultEnums.MeasureUnit	units Units used in measurements, default is pixels.

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

configurationEventlistenerList, controlEventlistenerList, notifyListenersRecursively, operatorExecStatus, stepSize, stepWiseExecution

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
Mica2D() Default constructor.
Mica2D(MTBImage img, int nc, int cc) Default constructor.

Method Summary

Modifier and Type	Method and Description
String	getDocumentation()
SegResult_Complete	getResultData() Returns result data object.
String	getSaveIntermediateResultPath() Returns path where to save intermediate results.
protected void	operate() Invokes analysis procedure on given image.
private MTBImageRGB	prepareResultImageStack() Initialize result image stack.
void	saveIntermediateResults(boolean flag) Set flag to save intermediate results.
void	setChannelsToCopy(int[] carray) Specify list of channels to copy to result stack.
void	setDoGauss(boolean _doGauss) Specify if cell channel is to be smoothed prior to detection.
void	setGaussSigma(double _gaussSigma) Specify sigma for Gaussian smoothing.
void	setInitialSnakes(MTBPolygon2DSet f) Specify set of initial snakes.
void	setMeasureUnits(SegResultEnums.MeasureUnit mu) Specify how to measure lengths and areas.
void	setSaveIntermediateResultPath(String sIntermediateResultPath) Set path where to save intermediate results.
void	showIntermediateResults(boolean flag) Set flag to display intermediate results.
void	showMasksOnly(boolean flag) Set flag indicating whether to show masks or overlays in result stack.
boolean	supportsStepWiseExecution()

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable

addALDConfigurationEventListener, addALDControlEventListener, fireALDConfigurationEvent, fireALDControlEvent, getControlStatus, getControlStatusHandle, getExecutionStatus, handleALDConfigurationEvent, handleALDControlEvent, removeALDConfigurationEventListener, removeALDControlEventListener, setControlStatus, setNotifyRecursiveFlag

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, readResolve, 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

inImg

@Parameter(label="Input image",
           required=true,
           direction=IN,
           description="Input image",
           dataIOOrder=-20)
private transient MTBImage inImg

Multi-channel input image.

nucleiChannel

@Parameter(label="Nucleus channel",
           required=true,
           dataIOOrder=-19,
           direction=IN,
           description="Nuclei channel (index starts with 1, -1 if none available).")
private int nucleiChannel

Nuclei channel.

cellChannel

@Parameter(label="Cytoplasm channel",
           required=true,
           dataIOOrder=-18,
           direction=IN,
           description="Cytoplasm channel, index starts with 1.")
private int cellChannel

Channel for cell boundary detection.

nucleiDetector

@Parameter(label="Nuclei detector",
           required=false,
           dataIOOrder=-20,
           direction=IN,
           description="Nucleus detector.")
private NucleusDetector2D nucleiDetector

Operator for nucleus detection/separation.

nucleiContours

@Parameter(label="Nuclei contours",
           required=false,
           dataIOOrder=-19,
           direction=IN,
           description="(Optional) set of nuclei contours.")
private MTBPolygon2DSet nucleiContours

(Optional) initial snake contours for nuclei.

If a nucleus channel is available contours can be extracted automatically.

cytoDetector

@Parameter(label="Cytoplasm detector",
           required=false,
           dataIOOrder=-18,
           direction=IN,
           description="Cytoplasm detector.")
private CytoplasmAnalyzer2D cytoDetector

Cytoplasma detection operator.

doGauss

@Parameter(label="Apply Gauss to cytoplasm channel",
           required=false,
           direction=IN,
           dataIOOrder=-17,
           description="Apply Gaussian smoothing to cytoplasm channel.")
private boolean doGauss

Preprocess cytoplasm channel by Gaussian smoothing.

gaussSigma

@Parameter(label="Gauss sigma",
           required=false,
           direction=IN,
           description="Sigma for Gaussian smoothing.",
           dataIOOrder=-16)
private double gaussSigma

Sigma for Gaussian smoothing.

particleDetector

@Parameter(label="Particle detector",
           required=false,
           dataIOOrder=-15,
           direction=IN,
           description="Minimum size of particles.")
private MultiChannelParticleAnalyzer2D particleDetector

Particle detector.

excludeParticlesInNuclei

@Parameter(label="Ignore particles in nuclei regions",
           required=false,
           dataIOOrder=-14,
           direction=IN,
           description="Ignore particles in nucleis.")
private boolean excludeParticlesInNuclei

Flag to ignore particle in nuclei regions.

units

@Parameter(label="Measure Units",
           required=false,
           direction=IN,
           dataIOOrder=-10,
           description="Units for measuring areas and sizes.")
private SegResultEnums.MeasureUnit units

Units used in measurements, default is pixels.

resultData

@Parameter(label="Result data summary",
           direction=OUT,
           description="Result segmentation masks.")
private transient SegResult_Complete resultData

Result data object.

resultStats

@Parameter(label="Table of result statistics",
           direction=OUT,
           description="Result statistical data.")
private transient Mica2DTableModel resultStats

Result data object.

prepareFinalResultStack

@Parameter(label="Show final result image stack",
           direction=IN,
           supplemental=true,
           dataIOOrder=-30,
           mode=STANDARD,
           description="Flag to enable result image stack display.")
private boolean prepareFinalResultStack

Flag for preparing final result image(s) stack.

showIntermediateResults

@Parameter(label="Show intermediate results",
           direction=IN,
           supplemental=true,
           dataIOOrder=-20,
           description="Flag for showing intermediate result image(s)/data.")
private boolean showIntermediateResults

Flag for showing intermediate results.

Be careful when using this option remote from commandline!

saveIntermediateResults

@Parameter(label="Save intermediate results",
           direction=IN,
           supplemental=true,
           dataIOOrder=-19,
           mode=ADVANCED,
           description="Flag for saving intermediate result image(s)/data.")
private boolean saveIntermediateResults

Flag for saving intermediate results to a specified directory.

saveIntermediateResultPath

@Parameter(label="Save intermediate results to...",
           direction=IN,
           supplemental=true,
           dataIOOrder=-18,
           mode=ADVANCED,
           description="Path where to save intermediate results.")
private de.unihalle.informatik.Alida.datatypes.ALDDirectoryString saveIntermediateResultPath

Path where to save intermediate results.

channelsToCopy

@Parameter(label="List of channel IDs to copy to result",
           supplemental=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=-15,
           description="Array of image channels to copy to result stack.")
private int[] channelsToCopy

Set of image channels to copy into result stack.

imagesAsMasks

@Parameter(label="Show b/w masks",
           dataIOOrder=-16,
           direction=IN,
           supplemental=true,
           mode=ADVANCED,
           description="Flag for showing masks only instead of overlays.")
private boolean imagesAsMasks

If flag is true, only masks are copied to result stack.

resultDataCells

private transient SegResult_Cytoplasm resultDataCells

Local container for cell cytoplasm segmentation result.

resultImages

private transient Vector<MTBImage> resultImages

Local container for set of segmentation result and channel copy images.

Constructor Detail

Mica2D

public Mica2D()
       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Mica2D

public Mica2D(MTBImage img,
              int nc,
              int cc)
       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Parameters:

img - Input multi-layer image to be processed.

nc - Nuclei channel.

cc - Cytoplasm channel.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

supportsStepWiseExecution

public boolean supportsStepWiseExecution()

Specified by:

supportsStepWiseExecution in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable

setInitialSnakes

public void setInitialSnakes(MTBPolygon2DSet f)

Specify set of initial snakes.

showIntermediateResults

public void showIntermediateResults(boolean flag)

Set flag to display intermediate results.

saveIntermediateResults

public void saveIntermediateResults(boolean flag)

Set flag to save intermediate results.

getSaveIntermediateResultPath

public String getSaveIntermediateResultPath()

Returns path where to save intermediate results.

setSaveIntermediateResultPath

public void setSaveIntermediateResultPath(String sIntermediateResultPath)

Set path where to save intermediate results.

setChannelsToCopy

public void setChannelsToCopy(int[] carray)

Specify list of channels to copy to result stack.

showMasksOnly

public void showMasksOnly(boolean flag)

Set flag indicating whether to show masks or overlays in result stack.

setMeasureUnits

public void setMeasureUnits(SegResultEnums.MeasureUnit mu)

Specify how to measure lengths and areas.

setDoGauss

public void setDoGauss(boolean _doGauss)

Specify if cell channel is to be smoothed prior to detection.

setGaussSigma

public void setGaussSigma(double _gaussSigma)

Specify sigma for Gaussian smoothing.

getResultData

public SegResult_Complete getResultData()

Returns result data object.

operate

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

Invokes analysis procedure on given image.

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

prepareResultImageStack

private MTBImageRGB prepareResultImageStack()

Initialize result image stack.

Transfers result images and selected input channels to a multi-channel RGB image.

getDocumentation

public String getDocumentation()

Overrides:

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