excludeLabelsOutsideSizeRange

Removes labels from a label map which are not within a certain size range.

Size of the labels is given as the number of pixel or voxels per label.

Availability: Available in Fiji by activating the update sites clij and clij2. This function is part of clij2_-2.5.0.1.jar.

excludeLabelsOutsideSizeRange is often followed by

excludeLabelsWithValuesOutOfRange (1)

Usage in ImageJ macro

Ext.CLIJ2_excludeLabelsOutsideSizeRange(Image input, Image destination, Number minimum_size, Number maximum_size);

Usage in object oriented programming languages

Java

// init CLIJ and GPU
import net.haesleinhuepf.clij2.CLIJ2;
import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
CLIJ2 clij2 = CLIJ2.getInstance();

// get input parameters
ClearCLBuffer input = clij2.push(inputImagePlus);
destination = clij2.create(input);
float minimum_size = 1.0;
float maximum_size = 2.0;

// Execute operation on GPU
clij2.excludeLabelsOutsideSizeRange(input, destination, minimum_size, maximum_size);

// show result
destinationImagePlus = clij2.pull(destination);
destinationImagePlus.show();

// cleanup memory on GPU
clij2.release(input);
clij2.release(destination);

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
input = clij2.pushMat(input_matrix);
destination = clij2.create(input);
minimum_size = 1.0;
maximum_size = 2.0;

% Execute operation on GPU
clij2.excludeLabelsOutsideSizeRange(input, destination, minimum_size, maximum_size);

% show result
destination = clij2.pullMat(destination)

% cleanup memory on GPU
clij2.release(input);
clij2.release(destination);

Icy JavaScript

// init CLIJ and GPU
importClass(net.haesleinhuepf.clicy.CLICY);
importClass(Packages.icy.main.Icy);

clij2 = CLICY.getInstance();

// get input parameters
input_sequence = getSequence();
input = clij2.pushSequence(input_sequence);
destination = clij2.create(input);
minimum_size = 1.0;
maximum_size = 2.0;

// Execute operation on GPU
clij2.excludeLabelsOutsideSizeRange(input, destination, minimum_size, maximum_size);

// show result
destination_sequence = clij2.pullSequence(destination)
Icy.addSequence(destination_sequence);
// cleanup memory on GPU
clij2.release(input);
clij2.release(destination);

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.exclude_labels_outside_size_range(input, destination, minimum_size, maximum_size)

Example notebooks

parametric_images

Example scripts

parametric_images.ijm

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