inra.ijpb.plugins

Class MarkerControlledWatershed3DPlugin

java.lang.Object

inra.ijpb.plugins.MarkerControlledWatershed3DPlugin

All Implemented Interfaces:

ij.plugin.PlugIn

public class MarkerControlledWatershed3DPlugin
extends Object
implements ij.plugin.PlugIn

A plugin to perform marker-controlled watershed on a 2D or 3D image. References: [1] Fernand Meyer and Serge Beucher. "Morphological segmentation." Journal of visual communication and image representation 1.1 (1990): 21-46. [2] Peer Neubert and Peter Protzel. "Compact Watershed and Preemptive SLIC: On improving trade-offs of superpixel segmentation algorithms." 22nd international conference on pattern recognition. IEEE, 2014.

Author:

Ignacio Arganda-Carreras

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	binaryMarkers flag set to TRUE if markers are binary, to FALSE if markers are labels
static double	compactness compactness constraint, c parameter in compact watershed algorithm [2]
static boolean	getDams flag to calculate watershed dams
static boolean	use26neighbors flag to use 26-connectivity

Constructor Summary

Constructors

Constructor and Description
MarkerControlledWatershed3DPlugin()

Method Summary

Modifier and Type	Method and Description
ij.ImagePlus	process(ij.ImagePlus input, ij.ImagePlus marker, ij.ImagePlus mask, int connectivity) Apply marker-controlled watershed to a grayscale 2D or 3D image.
ij.ImagePlus	process(ij.ImagePlus input, ij.ImagePlus marker, ij.ImagePlus mask, int connectivity, double compactness) Apply marker-controlled watershed to a grayscale 2D or 3D image.
void	run(String arg) Plugin run method to be called from ImageJ

Methods inherited from class java.lang.Object

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

Field Detail

binaryMarkers

public static boolean binaryMarkers

flag set to TRUE if markers are binary, to FALSE if markers are labels

getDams

public static boolean getDams

flag to calculate watershed dams

use26neighbors

public static boolean use26neighbors

flag to use 26-connectivity

compactness

public static double compactness

compactness constraint, c parameter in compact watershed algorithm [2]

Constructor Detail

MarkerControlledWatershed3DPlugin

public MarkerControlledWatershed3DPlugin()

Method Detail

process

public ij.ImagePlus process(ij.ImagePlus input,
                            ij.ImagePlus marker,
                            ij.ImagePlus mask,
                            int connectivity)

Apply marker-controlled watershed to a grayscale 2D or 3D image.

Parameters:

input - grayscale 2D or 3D image (in principle a "gradient" image)

marker - the labeled marker image

mask - binary mask to restrict region of interest

connectivity - 6 or 26 voxel connectivity

Returns:

the resulting watershed

process

public ij.ImagePlus process(ij.ImagePlus input,
                            ij.ImagePlus marker,
                            ij.ImagePlus mask,
                            int connectivity,
                            double compactness)

Apply marker-controlled watershed to a grayscale 2D or 3D image.

Parameters:

input - grayscale 2D or 3D image (in principle a "gradient" image)

marker - the labeled marker image

mask - binary mask to restrict region of interest

connectivity - 6 or 26 voxel connectivity

compactness - compactness constraint for compact watershed (set to 0 for classical watershed)

Returns:

the resulting watershed

run

public void run(String arg)

Plugin run method to be called from ImageJ

Specified by:

run in interface ij.plugin.PlugIn