simpleITKConnectedComponent

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

Apply SimpleITKs ConnectedComponent to an image.

See also: https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1ConnectedComponentImageFilter.html

Category: Labels

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_simpleITKConnectedComponent(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.simpleITKConnectedComponent(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.simpleITKConnectedComponent(input, destination);

% show result
destination = clijx.pullMat(destination)

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

Example notebooks

count_blobs.ipynb
spots_pointlists_matrices_tables.ipynb
napari_dask.ipynb
bead_segmentation.ipynb
parametric_maps.ipynb
tribolium_morphometry.ipynb
connected_component_labeling.ipynb

Example scripts

count_blobs.py
napari_.py
napari_magicgui.py
tribolium.py

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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