thresholdDefault

By Robert Haase based on work by G. Landini and W. Rasband

The automatic thresholder utilizes the Default threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

Categories: Segmentation, Binary

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

thresholdDefault often follows after

gaussianBlur3D (1)

thresholdDefault is often followed by

binaryNot (1)
release (3)

Usage in ImageJ macro

Ext.CLIJ2_thresholdDefault(Image input, Image destination);

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);

// Execute operation on GPU
clij2.thresholdDefault(input, destination);

// 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);

% Execute operation on GPU
clij2.thresholdDefault(input, destination);

% 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);

// Execute operation on GPU
clij2.thresholdDefault(input, destination);

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

License terms

The code for the automatic thresholding methods originates from https://github.com/imagej/imagej1/blob/master/ij/process/AutoThresholder.java

Detailed documentation on the implemented methods can be found online: https://imagej.net/Auto_Threshold

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