simpleITKOtsuThreshold

By Robert Haase, based on work by Bradley Lowekamp and the SimpleITK and ITK teams

Apply SimpleITKs Otsu Thresholding to an image.

Compared to SimpleITKs implementation, results are inverted to match ImageJs behaviour. See also: https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1OtsuThresholdImageFilter.html

Categories: Binary, Segmentation

Availability: Available in Fiji by activating the update sites clij, clij2 and clijx-assistant-extensions. This function is part of clijx-assistant-simpleitk_-0.6.0.1.jar.

Usage in ImageJ macro

Ext.CLIJx_simpleITKOtsuThreshold(Image input, Image destination);

Usage in object oriented programming languages

Java

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

// get input parameters
ClearCLBuffer input = clijx.push(inputImagePlus);
destination = clijx.create(input);

// Execute operation on GPU
clijx.simpleITKOtsuThreshold(input, destination);

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

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

Matlab

% init CLIJ and GPU
clijx = init_clatlabx();

% get input parameters
input = clijx.pushMat(input_matrix);
destination = clijx.create(input);

% Execute operation on GPU
clijx.simpleITKOtsuThreshold(input, destination);

% show result
destination = clijx.pullMat(destination)

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

License terms

This plugin is licensed BSD3, see:
https://github.com/clij/clijx-assistant-simpleitk/blob/master/license.txt
The underlying SimpleITK librariy is Apache 2 licensed:
https://github.com/SimpleITK/SimpleITK/blob/master/LICENSE

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