modeOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the most popular integer value among touching neighbors for every object. TODO: This only works for values between 0 and 255 for now.

Availability: Available in Fiji by activating the update sites clij and clij2. This function is part of clijx_-0.30.1.21.jar.

Usage in ImageJ macro

Ext.CLIJx_modeOfTouchingNeighbors(Image values, Image touch_matrix, Image mode_values_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 values = clijx.push(valuesImagePlus);
ClearCLBuffer touch_matrix = clijx.push(touch_matrixImagePlus);
mode_values_destination = clijx.create(values);

// Execute operation on GPU
clijx.modeOfTouchingNeighbors(values, touch_matrix, mode_values_destination);

// show result
mode_values_destinationImagePlus = clijx.pull(mode_values_destination);
mode_values_destinationImagePlus.show();

// cleanup memory on GPU
clijx.release(values);
clijx.release(touch_matrix);
clijx.release(mode_values_destination);

Matlab

% init CLIJ and GPU
clijx = init_clatlabx();

% get input parameters
values = clijx.pushMat(values_matrix);
touch_matrix = clijx.pushMat(touch_matrix_matrix);
mode_values_destination = clijx.create(values);

% Execute operation on GPU
clijx.modeOfTouchingNeighbors(values, touch_matrix, mode_values_destination);

% show result
mode_values_destination = clijx.pullMat(mode_values_destination)

% cleanup memory on GPU
clijx.release(values);
clijx.release(touch_matrix);
clijx.release(mode_values_destination);

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.mode_of_touching_neighbors(values, touch_matrix, mode_values_destination)

Example notebooks

tissue_neighborhood_quantification.ipynb

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