org.incenp.imagej

Class NucleiSegmenter

java.lang.Object

org.incenp.imagej.NucleiSegmenter

public class NucleiSegmenter
extends Object

This class provides methods implementing the Watershed segmentation of cell nuclei as described in https://imagej.net/Nuclei_Watershed_Separation.

Constructor Summary

Constructors

Constructor and Description
NucleiSegmenter(double radius) Creates a new nuclei segmenter with the “Moments” thresholding algorithm.
NucleiSegmenter(double radius, ij.process.AutoThresholder.Method thresholding) Creates a new nuclei segmenter.

Method Summary

Modifier and Type	Method and Description
ij.ImagePlus	segment(ij.ImagePlus image) Segments an entire hyperstack.
ij.ImagePlus	segment(ij.ImagePlus image, int[] channels) Segments a hyperstack, including all slices and all frames.
ij.ImagePlus	segment(ij.ImagePlus image, int[] channels, int[] slices, int[] frames) Segments a hyperstack.
ij.process.ImageProcessor	segment(ij.process.ImageProcessor ip) Segments a single image.

Methods inherited from class java.lang.Object

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

Constructor Detail

NucleiSegmenter

public NucleiSegmenter(double radius,
                       ij.process.AutoThresholder.Method thresholding)

Creates a new nuclei segmenter.

Parameters:

radius - the radius for the gaussian blur filtering step

thresholding - the automatic thresholding algorithm to use

NucleiSegmenter

public NucleiSegmenter(double radius)

Creates a new nuclei segmenter with the “Moments” thresholding algorithm.

Parameters:

radius - the radius for the gaussian blur filtering step.

Method Detail

segment

public ij.process.ImageProcessor segment(ij.process.ImageProcessor ip)

Segments a single image.

Parameters:

ip - the source image to segment

Returns:

a binary image containing the segmented nuclei

segment

public ij.ImagePlus segment(ij.ImagePlus image,
                            int[] channels,
                            int[] slices,
                            int[] frames)

Segments a hyperstack.

Parameters:

image - the source image to segment

channels - the list of channels to process

slices - the list of Z-slices to process

frames - the list of Z-frames to process

Returns:

a hyperstack containing the segmented binary images

segment

public ij.ImagePlus segment(ij.ImagePlus image,
                            int[] channels)

Segments a hyperstack, including all slices and all frames.

Parameters:

image - the source image to segment

channels - the list of channels to process

Returns:

a hyperstack containing the segmented binary images

segment

public ij.ImagePlus segment(ij.ImagePlus image)

Segments an entire hyperstack.

Parameters:

image - the source image to segment

Returns:

a hyperstack containing the segmented binary images