de.unihalle.informatik.MiToBo.apps.cytoplasm2D

Class CytoplasmAnalyzer2D

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.cytoplasm2D.CytoplasmAnalyzer2D

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="Segment cell contours from a given single-layer image.")
public class CytoplasmAnalyzer2D
extends MTBOperatorControllable

Operator to segment cell contours from a given single-layer image.

This operator allows to iteratively segment cell membrane and cytoplasm, respectively. It basically relies on snakes applying them either in an iterative fashion or without iterative levels. In the first case between the different snake runs the segmented cell regions are expanded by voronoi dilation and their internal areas are masked to enforce further region growth by decreasing the regions' average intensity values.

Further details about the iterative method can be found in the paper: B. Möller, N. Stöhr, S. Hüttelmaier and S. Posch, "Cascaded Segmentation of Grained Cell Tissue with Active Contour Models". In Proc. of Int. Conf. on Pattern Recognition (ICPR '10), August 2010.

Details about the non-iterative approach can be found in: B. Möller and S. Posch, "MiCA - Easy Cell Image Analysis with Normalized Snakes". In Proc. of Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB '11), Heidelberg, Germany, Sep. 2011.

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CytoplasmAnalyzer2D.DetectMode Operator mode.

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
protected boolean[]	activeSnakes Array with active snakes.
protected int[]	colorArray Array with colors for visualization.
protected MTBPolygon2DSet	currentSnakes Current set of snakes.
protected CytoplasmAnalyzer2D.DetectMode	detectionMode Operator mode to run.
private int	height
protected MTBImage	inImg Single-layer input image to be processed.
protected MTBPolygon2DSet	initialSnakes Initial snakes for cells, e.g. nuclei contours.
private MTBImageByte	labelImg
protected int	maxExpansion Maximum expansion by Voronoi dilation.
protected int	maxLevels Maximum number of levels to perform.
protected double	minAreaGrowth Lower threshold for region growth.
protected double	minIntensityVariance Minimum admissible variance in new snake interior fractions..
private static int	MinSnakePointNum Minimum number of points acceptable for snakes.
protected SegResult_Cytoplasm	resultData Result data object.
protected MTBImageRGB	resultImage Result segmentation image.
protected MTBPolygon2DSet	resultSnakes
protected boolean	saveIntermediateResults Flag for saving intermediate results.
protected String	saveIntermediateResultsPath Path where to save intermediate results.
protected boolean	showIntermediateResults Flag for displaying intermediate results.
private int[]	snakeArea
private int	snakeNum Number of snakes.
protected SnakeOptimizerCoupled	snakeOpter Snake optimizer.
private int	width

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
CytoplasmAnalyzer2D() Default constructor.
CytoplasmAnalyzer2D(MTBImage img, MTBPolygon2DSet initS, SnakeOptimizerCoupled snakeObj, CytoplasmAnalyzer2D.DetectMode m, int _maxLevels) Default constructor.

Method Summary

Modifier and Type	Method and Description
void	disableSaveIntermediateResults() Do not save intermediate results.
void	disableShowIntermediateResults() Disable display of intermediate results.
void	enableSaveIntermediateResults() Save intermediate results.
void	enableShowIntermediateResults() Enable display of intermediate results.
String	getDocumentation()
int	getMaxLevels() Returns maximum number of levels in iterative mode.
SegResult_Cytoplasm	getResultData() Returns result data object.
protected void	operate()
private void	runIterativeMode() Cell tissue segmentation in an iterative fashion.
private void	runMeanVarMode() Deprecated.
void	setDetectionMode(CytoplasmAnalyzer2D.DetectMode m) Specify detection mode.
void	setInitialSnakes(MTBPolygon2DSet snakes) Specify initial snakes.
void	setInputImage(MTBImage img) Specify input image.
void	setIntermediateResultDirectory(String dir) Set intermediate result directory.
void	setMaxLevels(int maxL) Specify maximum number of levels for iterative mode.
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,
           mode=STANDARD)
protected transient MTBImage inImg

Single-layer input image to be processed.

initialSnakes

@Parameter(label="Initial snake(s)",
           required=true,
           direction=IN,
           description="Initial snakes.",
           dataIOOrder=-19,
           mode=STANDARD)
protected MTBPolygon2DSet initialSnakes

Initial snakes for cells, e.g. nuclei contours.

snakeOpter

@Parameter(label="Snake optimizer",
           required=true,
           direction=IN,
           description="Snake optimizer object.",
           dataIOOrder=-18,
           mode=STANDARD)
protected SnakeOptimizerCoupled snakeOpter

Snake optimizer.

detectionMode

@Parameter(label="Operation mode",
           required=false,
           direction=IN,
           description="Mode of operation.",
           dataIOOrder=-15,
           mode=ADVANCED)
protected CytoplasmAnalyzer2D.DetectMode detectionMode

Operator mode to run.

maxLevels

@Parameter(label="Max. level count",
           required=false,
           direction=IN,
           description="Maximum levels in iterative mode.",
           dataIOOrder=-14,
           mode=ADVANCED)
protected int maxLevels

Maximum number of levels to perform.

maxExpansion

@Parameter(label="Max. distance in voronoi expansion",
           required=false,
           direction=IN,
           description="Maximum expansion during Voronoi dilation.",
           dataIOOrder=-13,
           mode=ADVANCED)
protected int maxExpansion

Maximum expansion by Voronoi dilation.

minAreaGrowth

@Parameter(label="Min. area growth",
           required=false,
           direction=IN,
           description="Minimum admissible area growth between iterations.",
           dataIOOrder=-12,
           mode=ADVANCED)
protected double minAreaGrowth

Lower threshold for region growth.

minIntensityVariance

@Parameter(label="Min. intensity variance",
           required=false,
           direction=IN,
           description="Minimum admissible area growth between iterations.",
           dataIOOrder=-11,
           mode=ADVANCED)
protected double minIntensityVariance

Minimum admissible variance in new snake interior fractions..

resultImage

@Parameter(label="Result image",
           required=true,
           direction=OUT,
           description="Result image showing snakes in overlay.")
protected transient MTBImageRGB resultImage

Result segmentation image.

resultData

@Parameter(label="Result Statistics",
           required=true,
           direction=OUT,
           description="Result data object.")
protected transient SegResult_Cytoplasm resultData

Result data object.

showIntermediateResults

@Parameter(label="Show intermediate results",
           supplemental=true,
           direction=IN,
           dataIOOrder=-3,
           description="Show intermediate results to user.")
protected boolean showIntermediateResults

Flag for displaying intermediate results.

saveIntermediateResults

@Parameter(label="Save intermediate results",
           supplemental=true,
           direction=IN,
           dataIOOrder=-2,
           description="Save intermediate results to disc.")
protected boolean saveIntermediateResults

Flag for saving intermediate results.

saveIntermediateResultsPath

@Parameter(label="Save intermediate results path",
           supplemental=true,
           direction=IN,
           dataIOOrder=-1,
           description="Path for saving (intermediate) results.")
protected String saveIntermediateResultsPath

Path where to save intermediate results.

resultSnakes

@Parameter(label="Result snakes",
           direction=OUT,
           description="Final snakes.",
           required=false)
protected transient MTBPolygon2DSet resultSnakes

MinSnakePointNum

private static final int MinSnakePointNum

Minimum number of points acceptable for snakes.

See Also:

Constant Field Values

snakeNum

private transient int snakeNum

Number of snakes.

activeSnakes

protected transient boolean[] activeSnakes

Array with active snakes.

colorArray

protected transient int[] colorArray

Array with colors for visualization.

currentSnakes

protected transient MTBPolygon2DSet currentSnakes

Current set of snakes.

labelImg

private transient MTBImageByte labelImg

width

private transient int width

height

private transient int height

snakeArea

private transient int[] snakeArea

Constructor Detail

CytoplasmAnalyzer2D

public CytoplasmAnalyzer2D()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

CytoplasmAnalyzer2D

public CytoplasmAnalyzer2D(MTBImage img,
                           MTBPolygon2DSet initS,
                           SnakeOptimizerCoupled snakeObj,
                           CytoplasmAnalyzer2D.DetectMode m,
                           int _maxLevels)
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Parameters:

inImg - Image to work on.

initS - Set of initial contours.

snakeObj - Snake parameter configuration object.

m - Detection mode.

maxLevels - Maximum number of levels.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

supportsStepWiseExecution

public boolean supportsStepWiseExecution()

Specified by:

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

setInputImage

public void setInputImage(MTBImage img)

Specify input image.

setInitialSnakes

public void setInitialSnakes(MTBPolygon2DSet snakes)

Specify initial snakes.

getMaxLevels

public int getMaxLevels()

Returns maximum number of levels in iterative mode.

setMaxLevels

public void setMaxLevels(int maxL)

Specify maximum number of levels for iterative mode.

setDetectionMode

public void setDetectionMode(CytoplasmAnalyzer2D.DetectMode m)

Specify detection mode.

enableShowIntermediateResults

public void enableShowIntermediateResults()

Enable display of intermediate results.

disableShowIntermediateResults

public void disableShowIntermediateResults()

Disable display of intermediate results.

enableSaveIntermediateResults

public void enableSaveIntermediateResults()

Save intermediate results.

disableSaveIntermediateResults

public void disableSaveIntermediateResults()

Do not save intermediate results.

setIntermediateResultDirectory

public void setIntermediateResultDirectory(String dir)

Set intermediate result directory.

getResultData

public SegResult_Cytoplasm getResultData()

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

runIterativeMode

private void runIterativeMode()
                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                              de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Cell tissue segmentation in an iterative fashion.

Initial contours are first expanded by dilation and then iteratively optimized using snakes. After each iteration region growth is assessed, and if it gets too small, segmentation terminates. If not, contours are again expanded and segmentation continues.

For details see:

• B. Möller, N. Stöhr, S. Hüttelmaier and S. Posch,
  "Cascaded Segmentation of Grained Cell Tissue with Active Contour Models", in Proc. of ICPR, 2010, pp. 1481-1484.
• B. Möller, O. Greß, N. Stöhr, S. Hüttelmaier and S. Posch,
  "Adaptive Segmentation of Cells and Particles in Fluorescent Microscope Images", Proc. of VISAPP, pp. 2:97-106, 2010.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

runMeanVarMode

@Deprecated
private void runMeanVarMode()
                                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                        de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Deprecated.

Cell tissue segmentation in an iterative fashion.

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