inra.ijpb.morphology

Class Reconstruction3D

java.lang.Object

inra.ijpb.morphology.Reconstruction3D

public abstract class Reconstruction3D
extends Object

Morphological reconstruction for 8-bits grayscale or binary stacks.

This class provides a collection of static methods for commonly used operations on 3D images, such as border removal or holes filling.

Example of use:

 ImageStack mask = IJ.getImage().getStack();
 int bitDepth = mask.getBitDepth();
 ImageStack marker = ImageStack.create(mask.getWidth(), mask.getHeight(), mask.getSize(), bitDepth);
 marker.set(30, 20, 10, 255); 
 ImageStack rec = Reconstruction3D.reconstructByDilation(marker, mask, 6);
 ImagePlus res = new ImagePlus("Reconstruction", rec);
 res.show(); 
 

Author:

David Legland

See Also:

Reconstruction, FloodFill3D

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	Reconstruction3D() Private constructor to prevent class instantiation.

Method Summary

Modifier and Type	Method and Description
static ij.ImageStack	fillHoles(ij.ImageStack image) Fills the holes in the input image, by (1) inverting the image, (2) performing a morphological reconstruction initialized with inverted image boundary and (3) by inverting the result.
static ij.ImageStack	killBorders(ij.ImageStack image) Removes the border of the input image, by performing a morphological reconstruction initialized with image boundary.
static ij.ImageStack	reconstructByDilation(ij.ImageStack marker, ij.ImageStack mask) Static method to computes the morphological reconstruction by dilation of the marker image under the mask image.
static ij.ImageStack	reconstructByDilation(ij.ImageStack marker, ij.ImageStack mask, int connectivity) Static method to computes the morphological reconstruction by dilation of the marker image under the mask image.
static ij.ImageStack	reconstructByDilation(ij.ImageStack marker, ij.ImageStack mask, int connectivity, ij.ImageStack binaryMask) Static method to computes the morphological reconstruction by dilation of the marker image under the mask image, but restricted to a binary mask.
static ij.ImageStack	reconstructByErosion(ij.ImageStack marker, ij.ImageStack mask) Static method to computes the morphological reconstruction by erosion of the marker image over the mask image.
static ij.ImageStack	reconstructByErosion(ij.ImageStack marker, ij.ImageStack mask, int connectivity) Static method to computes the morphological reconstruction by erosion of the marker image over the mask image.

Methods inherited from class java.lang.Object

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

Constructor Detail

Reconstruction3D

protected Reconstruction3D()

Private constructor to prevent class instantiation.

Method Detail

killBorders

public static final ij.ImageStack killBorders(ij.ImageStack image)

Removes the border of the input image, by performing a morphological reconstruction initialized with image boundary.

Parameters:

image - the image to process

Returns:

a new image with borders removed

See Also:

fillHoles(ImageStack)

fillHoles

public static final ij.ImageStack fillHoles(ij.ImageStack image)

Fills the holes in the input image, by (1) inverting the image, (2) performing a morphological reconstruction initialized with inverted image boundary and (3) by inverting the result.

Parameters:

image - the image to process

Returns:

a new image with holes filled

See Also:

killBorders(ImageStack)

reconstructByDilation

public static final ij.ImageStack reconstructByDilation(ij.ImageStack marker,
                                                        ij.ImageStack mask)

Static method to computes the morphological reconstruction by dilation of the marker image under the mask image.

Parameters:

marker - input marker image

mask - mask image

Returns:

the result of 3D morphological reconstruction

reconstructByDilation

public static final ij.ImageStack reconstructByDilation(ij.ImageStack marker,
                                                        ij.ImageStack mask,
                                                        int connectivity)

Static method to computes the morphological reconstruction by dilation of the marker image under the mask image.

Parameters:

marker - input marker image

mask - mask image

connectivity - 3d connectivity (6 or 26)

Returns:

the result of 3D morphological reconstruction

reconstructByDilation

public static final ij.ImageStack reconstructByDilation(ij.ImageStack marker,
                                                        ij.ImageStack mask,
                                                        int connectivity,
                                                        ij.ImageStack binaryMask)

Static method to computes the morphological reconstruction by dilation of the marker image under the mask image, but restricted to a binary mask.

Parameters:

marker - input marker image

mask - mask image

connectivity - 3d connectivity (6 or 26)

binaryMask - binary mask to restrict area of application

Returns:

morphological reconstruction by dilation of input image

reconstructByErosion

public static final ij.ImageStack reconstructByErosion(ij.ImageStack marker,
                                                       ij.ImageStack mask)

Static method to computes the morphological reconstruction by erosion of the marker image over the mask image.

Parameters:

marker - input marker image

mask - mask image

Returns:

the result of 3D morphological reconstruction

reconstructByErosion

public static final ij.ImageStack reconstructByErosion(ij.ImageStack marker,
                                                       ij.ImageStack mask,
                                                       int connectivity)

Static method to computes the morphological reconstruction by erosion of the marker image over the mask image.

Parameters:

marker - input marker image

mask - mask image

connectivity - 3d connectivity (6 or 26)

Returns:

the result of 3D morphological reconstruction