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reference_automaticThreshold.md

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automaticThreshold

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

The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method.

Enter one of these methods in the method text field: [Default, Huang, Intermodes, IsoData, IJ_IsoData, Li, MaxEntropy, Mean, MinError, Minimum, Moments, Otsu, Percentile, RenyiEntropy, Shanbhag, Triangle, Yen]

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.

automaticThreshold often follows after

automaticThreshold is often followed by

Usage in ImageJ macro

Ext.CLIJ2_automaticThreshold(Image input, Image destination, String method);

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.automaticThreshold(input, destination, method);

// 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.automaticThreshold(input, destination, method);

% 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.automaticThreshold(input, destination, method);

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

Example notebooks

compare_workflows
labeling
measure_overlap

Example scripts

boundingBoxes.ijm
center_of_mass.ijm
compare_workflows.ijm
excludeLabelsOnEdges.ijm
excludeLabelsWithinRange.ijm
intensity_per_label.ijm
labeling.ijm
measure_overlap.ijm
outline.ijm
particle_analysis.ijm
statistics.ijm
workflow.ijm
automaticThreshold.py
segmentation.py
statistics.py

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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