de.unihalle.informatik.MiToBo.apps.datatypes.cellImages

Class SegResult_Nuclei

java.lang.Object

de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei

All Implemented Interfaces:

SegResult_Interface

@ALDParametrizedClass
public class SegResult_Nuclei
extends Object
implements SegResult_Interface

Nuclei segmentation result from a single image channel.

Author:

moeller

Field Summary

Fields

Modifier and Type	Field and Description
protected double	avgsize_nuclei Average size of nuclei.
protected MTBImageByte	binMask Binary segmentation mask.
protected String	image_name Name of the analyzed image.
protected MTBImage	labelImage Gray-scale label image of nuclei regions.
protected MTBRegion2DSet	nucleiRegions Set of detected regions.
protected int	nucleusChannelID Index of the nucleus channel, if -1 it is unknown or image has only one.
protected int	number_nuclei Count of detected nuclei.
protected SegResultEnums.MeasureUnit	units Unit in which measurements are provided.

Constructor Summary

Constructors

Constructor and Description
SegResult_Nuclei(String imgName, int channel, MTBImageByte mask, MTBImage labels, MTBRegion2DSet regs, int count, double avgsize) Default constructor.

Method Summary

Modifier and Type	Method and Description
String	getImageName() Returns the name of the processed image.
MTBImage	getLabelImage() Returns label image of detected nuclei.
MTBImageByte	getMask() Returns binary mask with segmentation result.
SegResultEnums.MeasureUnit	getMeasurementUnit() Returns the unit of measurements.
double	getNucleiAvgSize() Returns average size of detected nuclei.
int	getNucleiCount() Returns number of detected nuclei.
MTBRegion2DSet	getNucleiRegions() Returns set of detected regions.
void	setLabelImage(MTBImage limg) Set label image of detected nuclei.
void	setMask(MTBImageByte m) Specify binary mask of nuclei.
void	setMeasurementUnit(SegResultEnums.MeasureUnit u) Specify unit for measurements.
void	setNucleiAvgSize(double avg) Specify average size of nuclei.
void	setNucleiCount(int c) Specify number of segmented nuclei regions.
void	setNucleiRegions(MTBRegion2DSet regs) Specify set of regions.
void	setNucleusChannel(int c) Specify image channel containing nuclei (just for reference).

Methods inherited from class java.lang.Object

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

Field Detail

image_name

@ALDClassParameter(label="Processed image",
                   dataIOOrder=-10)
protected String image_name

Name of the analyzed image.

binMask

@ALDClassParameter(label="Binary mask")
protected MTBImageByte binMask

Binary segmentation mask.

labelImage

@ALDClassParameter(label="Labeled nuclei regions")
protected MTBImage labelImage

Gray-scale label image of nuclei regions.

nucleiRegions

@ALDClassParameter(label="Set of nuclei regions",
                   dataIOOrder=-8)
protected MTBRegion2DSet nucleiRegions

Set of detected regions.

nucleusChannelID

@ALDClassParameter(label="Nucleus channel",
                   dataIOOrder=-9)
protected int nucleusChannelID

Index of the nucleus channel, if -1 it is unknown or image has only one.

number_nuclei

@ALDClassParameter(label="Number of nuclei",
                   dataIOOrder=-7)
protected int number_nuclei

Count of detected nuclei.

avgsize_nuclei

@ALDClassParameter(label="Average size",
                   dataIOOrder=-6)
protected double avgsize_nuclei

Average size of nuclei.

units

@ALDClassParameter(label="Measurement unit",
                   dataIOOrder=-5)
protected SegResultEnums.MeasureUnit units

Unit in which measurements are provided.

Constructor Detail

SegResult_Nuclei

public SegResult_Nuclei(String imgName,
                        int channel,
                        MTBImageByte mask,
                        MTBImage labels,
                        MTBRegion2DSet regs,
                        int count,
                        double avgsize)

Default constructor.

Parameters:

imgName - Name of processed image.

channel - Index of nucleus channel.

mask - Binary mask with segmentation result.

count - Number of detected nuclei.

avgsize - Average size of nuclei.

chan - Nucleus channel ID.

Method Detail

setNucleusChannel

public void setNucleusChannel(int c)

Specify image channel containing nuclei (just for reference).

Parameters:

c - Nucleus channel ID.

getImageName

public String getImageName()

Description copied from interface: SegResult_Interface

Returns the name of the processed image.

Specified by:

getImageName in interface SegResult_Interface

setMask

public void setMask(MTBImageByte m)

Specify binary mask of nuclei.

Parameters:

m - Binary mask of detected nuclei.

getMask

public MTBImageByte getMask()

Returns binary mask with segmentation result.

Returns:

Binary mask of segmented nuclei.

setLabelImage

public void setLabelImage(MTBImage limg)

Set label image of detected nuclei.

Parameters:

limg - Label image with detected nuclei.

getLabelImage

public MTBImage getLabelImage()

Returns label image of detected nuclei.

Returns:

Label image of segmentation result.

setNucleiRegions

public void setNucleiRegions(MTBRegion2DSet regs)

Specify set of regions.

Parameters:

Set - of detected nucleus regions.

getNucleiRegions

public MTBRegion2DSet getNucleiRegions()

Returns set of detected regions.

Returns:

Set of nucleus regions.

setNucleiCount

public void setNucleiCount(int c)

Specify number of segmented nuclei regions.

Parameters:

c - Number of detected nuclei.

getNucleiCount

public int getNucleiCount()

Returns number of detected nuclei.

Returns:

Count of detected nuclei.

setNucleiAvgSize

public void setNucleiAvgSize(double avg)

Specify average size of nuclei.

Parameters:

avg - Average size of detected nuclei.

getNucleiAvgSize

public double getNucleiAvgSize()

Returns average size of detected nuclei.

Returns:

Average size of detected nuclei.

getMeasurementUnit

public SegResultEnums.MeasureUnit getMeasurementUnit()

Description copied from interface: SegResult_Interface

Returns the unit of measurements.

Specified by:

getMeasurementUnit in interface SegResult_Interface

setMeasurementUnit

public void setMeasurementUnit(SegResultEnums.MeasureUnit u)

Specify unit for measurements.

Parameters:

u - Unit used for area and length measurements.