public class BinaryImages
extends java.lang.Object
LabelImages
Modifier and Type  Method and Description 

static ij.process.ImageProcessor 
areaOpening(ij.process.ImageProcessor image,
int nPixelMin)
Applies area opening on a binary image: creates a new binary image that
contains only particles with at least the specified number of pixels.

static ij.ImagePlus 
binarize(ij.ImagePlus imagePlus)
Converts a grayscale 2D or 3D image into a binary image by setting
nonzero elements to 255.

static ij.process.ImageProcessor 
binarize(ij.process.ImageProcessor image)
Converts a grayscale 2D image into a binary 2D image by setting nonzero
pixels to 255.

static ij.ImageStack 
binarize(ij.ImageStack image)
Converts a grayscale 3D image into a binary 3D image by setting nonzero
voxels to 255.

static ij.ImagePlus 
componentsLabeling(ij.ImagePlus imagePlus,
int conn,
int bitDepth)
Computes the labels in the binary 2D or 3D image contained in the given
ImagePlus, and computes the maximum label to set up the display range of
the resulting ImagePlus.

static ij.process.ImageProcessor 
componentsLabeling(ij.process.ImageProcessor image,
int conn,
int bitDepth)
Computes the labels of the connected components in the given planar
binary image.

static ij.ImageStack 
componentsLabeling(ij.ImageStack image,
int conn,
int bitDepth)
Computes the labels of the connected components in the given 3D binary
image.

static ij.ImagePlus 
distanceMap(ij.ImagePlus imagePlus)
Computes the distance map (or distance transform) from a binary image
processor.

static ij.process.ImageProcessor 
distanceMap(ij.process.ImageProcessor image)
Computes the distance map (or distance transform) from a binary image
processor.

static ij.process.FloatProcessor 
distanceMap(ij.process.ImageProcessor image,
float[] weights,
boolean normalize)
Computes the distance map from a binary image processor, by specifying
weights and normalization.

static ij.process.ShortProcessor 
distanceMap(ij.process.ImageProcessor image,
short[] weights,
boolean normalize)
Computes the distance map from a binary image processor, by specifying
weights and normalization.

static ij.ImageStack 
distanceMap(ij.ImageStack image)
Computes the distance map from a binary 3D image.

static ij.ImageStack 
distanceMap(ij.ImageStack image,
float[] weights,
boolean normalize)
Computes the distance map from a binary 3D image.

static ij.ImageStack 
distanceMap(ij.ImageStack image,
short[] weights,
boolean normalize)
Computes the distance map from a binary 3D image.

static ij.process.ImageProcessor 
geodesicDistanceMap(ij.process.ImageProcessor marker,
ij.process.ImageProcessor mask)
Computes the geodesic distance transform (or geodesic distance map) of a
binary image of marker, constrained to a binary mask.

static ij.process.ImageProcessor 
geodesicDistanceMap(ij.process.ImageProcessor marker,
ij.process.ImageProcessor mask,
float[] weights,
boolean normalize)
Computes the geodesic distance transform (or geodesic distance map) of a
binary image of marker, constrained to a binary mask.

static ij.process.ImageProcessor 
geodesicDistanceMap(ij.process.ImageProcessor marker,
ij.process.ImageProcessor mask,
short[] weights,
boolean normalize)
Computes the geodesic distance transform (or geodesic distance map) of a
binary image of marker, constrained to a binary mask.

static ij.ImagePlus 
keepLargestRegion(ij.ImagePlus imagePlus)
Returns a binary image that contains only the largest region.

static ij.process.ImageProcessor 
keepLargestRegion(ij.process.ImageProcessor image)
Returns a binary image that contains only the largest region.

static ij.ImageStack 
keepLargestRegion(ij.ImageStack image)
Returns a binary image that contains only the largest label.

static void 
removeLargestRegion(ij.ImagePlus imagePlus)
Returns a binary image in which the largest region has been replaced by
background.

static ij.process.ImageProcessor 
removeLargestRegion(ij.process.ImageProcessor image)
Returns a binary image in which the largest region has been replaced by
the background value.

static ij.ImageStack 
removeLargestRegion(ij.ImageStack image)
Returns a binary image in which the largest region has been replaced by
the background value.

static ij.ImagePlus 
sizeOpening(ij.ImagePlus imagePlus,
int minElementCount)
Applies size opening on a binary 2D or 3D image.

static ij.ImageStack 
volumeOpening(ij.ImageStack image,
int nVoxelMin)
Applies area opening on a binary image: creates a new binary image that
contains only particle with at least the specified number of voxels.

public static final ij.ImagePlus componentsLabeling(ij.ImagePlus imagePlus, int conn, int bitDepth)
imagePlus
 contains the 3D binary image stackconn
 the connectivity, either 4 or 8 for planar images, or 6 or 26
for 3D imagesbitDepth
 the number of bits used to create the result image (8, 16 or
32)java.lang.RuntimeException
 if the number of labels reaches the maximum number that can
be represented with this bitDepthConnectedComponentsLabeling
,
ConnectedComponentsLabeling3D
,
FloodFill
public static final ij.process.ImageProcessor componentsLabeling(ij.process.ImageProcessor image, int conn, int bitDepth)
image
 contains the binary image (any type is accepted)conn
 the connectivity, either 4 or 8bitDepth
 the number of bits used to create the result image (8, 16 or
32)java.lang.RuntimeException
 if the number of labels reaches the maximum number that can
be represented with this bitDepthConnectedComponentsLabeling
public static final ij.ImageStack componentsLabeling(ij.ImageStack image, int conn, int bitDepth)
image
 contains the 3D binary image (any type is accepted)conn
 the connectivity, either 6 or 26bitDepth
 the number of bits used to create the result stack (8, 16 or
32)java.lang.RuntimeException
 if the number of labels reaches the maximum number that can
be represented with this bitDepthConnectedComponentsLabeling3D
public static final ij.ImagePlus distanceMap(ij.ImagePlus imagePlus)
imagePlus
 an ImagePlus object containing a binary imageDistanceTransform
,
DistanceTransform3D
public static final ij.process.ImageProcessor distanceMap(ij.process.ImageProcessor image)
Computes the distance map (or distance transform) from a binary image processor. Distance is computed for each foreground (white) pixel, as the chamfer distance to the nearest background (black) pixel.
This method uses default 5x5 weights, and normalizes the resulting map. Result is given in a new instance of ShortProcessor.
image
 the input binary imagepublic static final ij.process.ShortProcessor distanceMap(ij.process.ImageProcessor image, short[] weights, boolean normalize)
Computes the distance map from a binary image processor, by specifying weights and normalization.
Distance is computed for each foreground (white) pixel, as the chamfer distance to the nearest background (black) pixel. Result is given as a new instance of ShortProcessor.
image
 the input binary imageweights
 an array of chamfer weights, with at least two valuesnormalize
 indicates whether the resulting distance map should be
normalized (divide distances by the first chamfer weight)public static final ij.process.FloatProcessor distanceMap(ij.process.ImageProcessor image, float[] weights, boolean normalize)
Computes the distance map from a binary image processor, by specifying weights and normalization.
Distance is computed for each foreground (white) pixel, as the chamfer distance to the nearest background (black) pixel. Result is given in a new instance of FloatProcessor.
image
 the input binary imageweights
 an array of chamfer weights, with at least two valuesnormalize
 indicates whether the resulting distance map should be
normalized (divide distances by the first chamfer weight)public static final ij.ImageStack distanceMap(ij.ImageStack image)
image
 the input binary imagepublic static final ij.ImageStack distanceMap(ij.ImageStack image, short[] weights, boolean normalize)
image
 the input binary imageweights
 an array of chamfer weights, with at least three valuesnormalize
 indicates whether the resulting distance map should be
normalized (divide distances by the first chamfer weight)public static final ij.ImageStack distanceMap(ij.ImageStack image, float[] weights, boolean normalize)
image
 the input 3D binary imageweights
 an array of chamfer weights, with at least three valuesnormalize
 indicates whether the resulting distance map should be
normalized (divide distances by the first chamfer weight)public static final ij.process.ImageProcessor geodesicDistanceMap(ij.process.ImageProcessor marker, ij.process.ImageProcessor mask)
marker
 the binary image of markermask
 the binary image of maskpublic static final ij.process.ImageProcessor geodesicDistanceMap(ij.process.ImageProcessor marker, ij.process.ImageProcessor mask, short[] weights, boolean normalize)
marker
 the binary image of markermask
 the binary image of maskweights
 an array of chamfer weights, with at least two valuesnormalize
 indicates whether the resulting distance map should be
normalized (divide distances by the first chamfer weight)public static final ij.process.ImageProcessor geodesicDistanceMap(ij.process.ImageProcessor marker, ij.process.ImageProcessor mask, float[] weights, boolean normalize)
marker
 the binary image of markermask
 the binary image of maskweights
 an array of chamfer weights, with at least two valuesnormalize
 indicates whether the resulting distance map should be
normalized (divide distances by the first chamfer weight)public static final ij.ImagePlus sizeOpening(ij.ImagePlus imagePlus, int minElementCount)
imagePlus
 the binary 2D or 3D image containing individual particlesminElementCount
 the minimum number of pixels or voxels required to keep a
particleLabelImages.sizeOpening(ImagePlus, int)
public static final ij.process.ImageProcessor areaOpening(ij.process.ImageProcessor image, int nPixelMin)
image
 the binary image containing individual particlesnPixelMin
 the minimum number of pixels required to keep a particleLabelImages.areaOpening(ImageProcessor, int)
public static final ij.ImageStack volumeOpening(ij.ImageStack image, int nVoxelMin)
image
 the 3D binary image containing individual particlesnVoxelMin
 the minimum number of voxels required to keep a particleLabelImages.volumeOpening(ImageStack, int)
public static final ij.ImagePlus keepLargestRegion(ij.ImagePlus imagePlus)
imagePlus
 an instance of imagePlus that contains a binary imagepublic static final ij.process.ImageProcessor keepLargestRegion(ij.process.ImageProcessor image)
image
 a binary image containing several individual regionspublic static final ij.ImageStack keepLargestRegion(ij.ImageStack image)
image
 a binary 3D image containing several individual regionspublic static final void removeLargestRegion(ij.ImagePlus imagePlus)
imagePlus
 a binary image containing several individual particlespublic static final ij.process.ImageProcessor removeLargestRegion(ij.process.ImageProcessor image)
image
 a binary image containing several individual particlespublic static final ij.ImageStack removeLargestRegion(ij.ImageStack image)
image
 a binary 3D image containing several individual particlespublic static final ij.ImagePlus binarize(ij.ImagePlus imagePlus)
imagePlus
 an ImagePlus object containing a gray scale imagepublic static final ij.process.ImageProcessor binarize(ij.process.ImageProcessor image)
image
 a gray scale imagepublic static final ij.ImageStack binarize(ij.ImageStack image)
image
 a gray scale 3D image