inra.ijpb.watershed

Class Watershed

java.lang.Object

inra.ijpb.watershed.Watershed

public class Watershed
extends Object

Several static methods for computing watershed in 2D/3D images.

Author:

Ignacio Arganda-Carreras

Constructor Summary

Constructors

Constructor and Description
Watershed()

Method Summary

Modifier and Type	Method and Description
static ij.ImagePlus	computeWatershed(ij.ImagePlus input, ij.ImagePlus marker, ij.ImagePlus binaryMask, int connectivity, boolean getDams) Compute watershed with markers with an optional binary mask to restrict the regions of application.
static ij.ImagePlus	computeWatershed(ij.ImagePlus input, ij.ImagePlus marker, ij.ImagePlus binaryMask, int connectivity, boolean getDams, boolean verbose) Compute watershed with markers with an optional binary mask to restrict the regions of application.
static ij.ImagePlus	computeWatershed(ij.ImagePlus input, ij.ImagePlus marker, ij.ImagePlus binaryMask, int connectivity, boolean getDams, double compactness, boolean verbose) Compute watershed with markers with an optional binary mask to restrict the regions of application.
static ij.ImagePlus	computeWatershed(ij.ImagePlus input, ij.ImagePlus mask, int connectivity) Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
static ij.ImagePlus	computeWatershed(ij.ImagePlus input, ij.ImagePlus marker, int connectivity, boolean getDams) Compute watershed with markers.
static ij.ImagePlus	computeWatershed(ij.ImagePlus input, ij.ImagePlus marker, int connectivity, boolean getDams, boolean verbose) Compute watershed with markers
static ij.ImagePlus	computeWatershed(ij.ImagePlus input, ij.ImagePlus mask, int connectivity, double hMin, double hMax) Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
static ij.ImagePlus	computeWatershed(ij.ImagePlus input, ij.ImagePlus mask, int connectivity, double hMin, double hMax, boolean verbose) Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
static ij.process.ImageProcessor	computeWatershed(ij.process.ImageProcessor input, ij.process.ImageProcessor mask, boolean verbose, int connectivity) Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
static ij.process.ImageProcessor	computeWatershed(ij.process.ImageProcessor input, ij.process.ImageProcessor marker, ij.process.ImageProcessor binaryMask, int connectivity, boolean getDams) Compute watershed with markers with an optional binary mask to restrict the regions of application.
static ij.process.ImageProcessor	computeWatershed(ij.process.ImageProcessor input, ij.process.ImageProcessor marker, ij.process.ImageProcessor binaryMask, int connectivity, boolean getDams, boolean verbose) Compute watershed with markers with an optional binary mask to restrict the regions of application.
static ij.process.ImageProcessor	computeWatershed(ij.process.ImageProcessor input, ij.process.ImageProcessor mask, int connectivity) Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
static ij.process.ImageProcessor	computeWatershed(ij.process.ImageProcessor input, ij.process.ImageProcessor marker, int connectivity, boolean getDams) Compute watershed with markers.
static ij.process.ImageProcessor	computeWatershed(ij.process.ImageProcessor input, ij.process.ImageProcessor marker, int connectivity, boolean getDams, boolean verbose) Compute watershed with markers.
static ij.ImageStack	computeWatershed(ij.ImageStack input, ij.ImageStack mask, boolean verbose, int connectivity) Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
static ij.ImageStack	computeWatershed(ij.ImageStack input, ij.ImageStack marker, ij.ImageStack binaryMask, int connectivity, boolean getDams) Compute watershed with markers with an optional binary mask to restrict the regions of application.
static ij.ImageStack	computeWatershed(ij.ImageStack input, ij.ImageStack marker, ij.ImageStack binaryMask, int connectivity, boolean getDams, boolean verbose) Compute watershed with markers with an optional binary mask to restrict the regions of application
static ij.ImageStack	computeWatershed(ij.ImageStack input, ij.ImageStack mask, int connectivity) Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
static ij.ImageStack	computeWatershed(ij.ImageStack input, ij.ImageStack marker, int connectivity, boolean getDams) Compute watershed with markers.
static ij.ImageStack	computeWatershed(ij.ImageStack input, ij.ImageStack marker, int connectivity, boolean getDams, boolean verbose) Compute watershed with markers.

Methods inherited from class java.lang.Object

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

Constructor Detail

Watershed

public Watershed()

Method Detail

computeWatershed

public static ij.ImagePlus computeWatershed(ij.ImagePlus input,
                                            ij.ImagePlus mask,
                                            int connectivity)

Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M. Vincent. "Determining watersheds in digital pictures via flooding simulations." Lausanne-DL tentative. International Society for Optics and Photonics, 1990.

Parameters:

input - original grayscale image (usually a gradient image)

mask - binary mask to restrict the regions of interest

connectivity - voxel connectivity to define neighborhoods

Returns:

image of labeled catchment basins with dams (labels are 1, 2, ...)

computeWatershed

public static ij.ImagePlus computeWatershed(ij.ImagePlus input,
                                            ij.ImagePlus mask,
                                            int connectivity,
                                            double hMin,
                                            double hMax)

Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M. Vincent. "Determining watersheds in digital pictures via flooding simulations." Lausanne-DL tentative. International Society for Optics and Photonics, 1990. Note: it outputs step messages in the Log window.

Parameters:

input - original grayscale image (usually a gradient image)

mask - binary mask to restrict the regions of interest

connectivity - voxel connectivity to define neighborhoods

hMin - the minimum value for dynamic

hMax - the maximum value for dynamic

Returns:

image of labeled catchment basins with dams (labels are 1, 2, ...)

computeWatershed

public static ij.ImagePlus computeWatershed(ij.ImagePlus input,
                                            ij.ImagePlus mask,
                                            int connectivity,
                                            double hMin,
                                            double hMax,
                                            boolean verbose)

Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M. Vincent. "Determining watersheds in digital pictures via flooding simulations." Lausanne-DL tentative. International Society for Optics and Photonics, 1990.

Parameters:

input - original grayscale image (usually a gradient image)

mask - binary mask to restrict the regions of interest

connectivity - voxel connectivity to define neighborhoods

hMin - the minimum value for dynamic

hMax - the maximum value for dynamic

verbose - flag to output step messages in Log window

Returns:

image of labeled catchment basins with dams (labels are 1, 2, ...)

computeWatershed

public static ij.ImageStack computeWatershed(ij.ImageStack input,
                                             ij.ImageStack mask,
                                             boolean verbose,
                                             int connectivity)

Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M. Vincent. "Determining watersheds in digital pictures via flooding simulations." Lausanne-DL tentative. International Society for Optics and Photonics, 1990.

Parameters:

input - original grayscale image (usually a gradient image)

mask - binary mask to restrict the regions of interest

verbose - flag to output step messages in Log window

connectivity - voxel connectivity to define neighborhoods

Returns:

image of labeled catchment basins with dams (labels are 1, 2, ...)

computeWatershed

public static ij.ImageStack computeWatershed(ij.ImageStack input,
                                             ij.ImageStack mask,
                                             int connectivity)

Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M. Vincent. "Determining watersheds in digital pictures via flooding simulations." Lausanne-DL tentative. International Society for Optics and Photonics, 1990. Note: it outputs step messages in the Log window.

Parameters:

input - original grayscale image (usually a gradient image)

mask - binary mask to restrict the regions of interest

connectivity - voxel connectivity to define neighborhoods

Returns:

image of labeled catchment basins with dams (labels are 1, 2, ...)

computeWatershed

public static ij.process.ImageProcessor computeWatershed(ij.process.ImageProcessor input,
                                                         ij.process.ImageProcessor mask,
                                                         boolean verbose,
                                                         int connectivity)

Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M. Vincent. "Determining watersheds in digital pictures via flooding simulations." Lausanne-DL tentative. International Society for Optics and Photonics, 1990.

Parameters:

input - original grayscale image (usually a gradient image)

mask - binary mask to restrict the regions of interest

verbose - flag to output step messages in Log window

connectivity - pixel connectivity to define neighborhoods (4 or 8)

Returns:

image of labeled catchment basins with dams (labels are 1, 2, ...)

computeWatershed

public static ij.process.ImageProcessor computeWatershed(ij.process.ImageProcessor input,
                                                         ij.process.ImageProcessor mask,
                                                         int connectivity)

Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M. Vincent. "Determining watersheds in digital pictures via flooding simulations." Lausanne-DL tentative. International Society for Optics and Photonics, 1990. Note: it outputs step messages in Log window.

Parameters:

input - original grayscale image (usually a gradient image)

mask - binary mask to restrict the regions of interest

connectivity - pixel connectivity to define neighborhoods (4 or 8)

Returns:

image of labeled catchment basins with dams (labels are 1, 2, ...)

computeWatershed

public static ij.ImagePlus computeWatershed(ij.ImagePlus input,
                                            ij.ImagePlus marker,
                                            ij.ImagePlus binaryMask,
                                            int connectivity,
                                            boolean getDams)

Compute watershed with markers with an optional binary mask to restrict the regions of application. Note: it outputs step messages in Log window.

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

binaryMask - binary mask to restrict the regions of interest

connectivity - voxel connectivity to define neighborhoods (4 or 8 for 2D, 6 or 26 for 3D)

getDams - select/deselect the calculation of dams

Returns:

image of labeled catchment basins (labels are 1, 2, ...)

computeWatershed

public static ij.ImagePlus computeWatershed(ij.ImagePlus input,
                                            ij.ImagePlus marker,
                                            ij.ImagePlus binaryMask,
                                            int connectivity,
                                            boolean getDams,
                                            boolean verbose)

Compute watershed with markers with an optional binary mask to restrict the regions of application.

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

binaryMask - binary mask to restrict the regions of interest

connectivity - voxel connectivity to define neighborhoods (4 or 8 for 2D, 6 or 26 for 3D)

getDams - select/deselect the calculation of dams

verbose - flag to display messages in the log window

Returns:

image of labeled catchment basins (labels are 1, 2, ...)

computeWatershed

public static ij.ImagePlus computeWatershed(ij.ImagePlus input,
                                            ij.ImagePlus marker,
                                            ij.ImagePlus binaryMask,
                                            int connectivity,
                                            boolean getDams,
                                            double compactness,
                                            boolean verbose)

Compute watershed with markers with an optional binary mask to restrict the regions of application. If the compactness constraint is larger than 0, the Compact Watershed algorithm will be executed (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).

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

binaryMask - binary mask to restrict the regions of interest

connectivity - voxel connectivity to define neighborhoods (4 or 8 for 2D, 6 or 26 for 3D)

getDams - select/deselect the calculation of dams

compactness - compactness constrain parameter (values larger than 0 involve using compact watershed)

verbose - flag to display messages in the log window

Returns:

image of labeled catchment basins (labels are 1, 2, ...)

computeWatershed

public static ij.ImageStack computeWatershed(ij.ImageStack input,
                                             ij.ImageStack marker,
                                             ij.ImageStack binaryMask,
                                             int connectivity,
                                             boolean getDams)

Compute watershed with markers with an optional binary mask to restrict the regions of application. Note: it outputs step messages in Log window.

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

binaryMask - binary mask to restrict the regions of interest

connectivity - voxel connectivity to define neighborhoods

getDams - select/deselect the calculation of dams

Returns:

image of labeled catchment basins (labels are 1, 2, ...)

computeWatershed

public static ij.ImageStack computeWatershed(ij.ImageStack input,
                                             ij.ImageStack marker,
                                             ij.ImageStack binaryMask,
                                             int connectivity,
                                             boolean getDams,
                                             boolean verbose)

Compute watershed with markers with an optional binary mask to restrict the regions of application

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

binaryMask - binary mask to restrict the regions of interest

connectivity - voxel connectivity to define neighborhoods

getDams - select/deselect the calculation of dams

verbose - flag to display messages in the log window

Returns:

image of labeled catchment basins (labels are 1, 2, ...)

computeWatershed

public static ij.process.ImageProcessor computeWatershed(ij.process.ImageProcessor input,
                                                         ij.process.ImageProcessor marker,
                                                         ij.process.ImageProcessor binaryMask,
                                                         int connectivity,
                                                         boolean getDams)

Compute watershed with markers with an optional binary mask to restrict the regions of application. Note: it outputs step messages in Log window.

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

binaryMask - binary mask to restrict the regions of interest

connectivity - voxel connectivity to define neighborhoods

getDams - select/deselect the calculation of dams

Returns:

image of labeled catchment basins (labels are 1, 2, ...)

computeWatershed

public static ij.process.ImageProcessor computeWatershed(ij.process.ImageProcessor input,
                                                         ij.process.ImageProcessor marker,
                                                         ij.process.ImageProcessor binaryMask,
                                                         int connectivity,
                                                         boolean getDams,
                                                         boolean verbose)

Compute watershed with markers with an optional binary mask to restrict the regions of application.

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

binaryMask - binary mask to restrict the regions of interest

connectivity - voxel connectivity to define neighborhoods

getDams - select/deselect the calculation of dams

verbose - flag to display log messages

Returns:

image of labeled catchment basins (labels are 1, 2, ...)

computeWatershed

public static ij.ImagePlus computeWatershed(ij.ImagePlus input,
                                            ij.ImagePlus marker,
                                            int connectivity,
                                            boolean getDams,
                                            boolean verbose)

Compute watershed with markers

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

connectivity - voxel connectivity to define neighborhoods

getDams - select/deselect the calculation of dams

verbose - flag to output step messages in Log window.

Returns:

image of labeled catchment basins (labels are 1, 2, ...)

computeWatershed

public static ij.ImagePlus computeWatershed(ij.ImagePlus input,
                                            ij.ImagePlus marker,
                                            int connectivity,
                                            boolean getDams)

Compute watershed with markers. Note: it outputs step messages in the Log window.

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

connectivity - voxel connectivity to define neighborhoods

getDams - select/deselect the calculation of dams

Returns:

image of labeled catchment basins (labels are 1, 2, ...)

computeWatershed

public static ij.ImageStack computeWatershed(ij.ImageStack input,
                                             ij.ImageStack marker,
                                             int connectivity,
                                             boolean getDams,
                                             boolean verbose)

Compute watershed with markers.

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

connectivity - voxel connectivity to define neighborhoods

getDams - select/deselect the calculation of dams

verbose - flag to output step message in the Log window

Returns:

image of labeled catchment basins (labels are 1, 2, ...)

computeWatershed

public static ij.ImageStack computeWatershed(ij.ImageStack input,
                                             ij.ImageStack marker,
                                             int connectivity,
                                             boolean getDams)

Compute watershed with markers. Note: it outputs step messages in the Low window.

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

connectivity - voxel connectivity to define neighborhoods

getDams - select/deselect the calculation of dams

Returns:

image of labeled catchment basins (labels are 1, 2, ...)

computeWatershed

public static ij.process.ImageProcessor computeWatershed(ij.process.ImageProcessor input,
                                                         ij.process.ImageProcessor marker,
                                                         int connectivity,
                                                         boolean getDams,
                                                         boolean verbose)

Compute watershed with markers.

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

connectivity - voxel connectivity to define neighborhoods

getDams - select/deselect the calculation of dams

verbose - flag to output step messages in the Low window

Returns:

image of labeled catchment basins (labels are 1, 2, ...)

computeWatershed

public static ij.process.ImageProcessor computeWatershed(ij.process.ImageProcessor input,
                                                         ij.process.ImageProcessor marker,
                                                         int connectivity,
                                                         boolean getDams)

Compute watershed with markers. Note: it outputs step message in the Low window.

Parameters:

input - original grayscale image (usually a gradient image)

marker - image with labeled markers

connectivity - voxel connectivity to define neighborhoods

getDams - select/deselect the calculation of dams

Returns:

image of labeled catchment basins (labels are 1, 2, ...)