medianOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the median value among touching neighbors for every object.

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

medianOfTouchingNeighbors often follows after

medianOfTouchingNeighbors is often followed by

standardDeviationOfTouchingNeighbors (1)
replaceIntensities (4)

Usage in ImageJ macro

Ext.CLIJ2_medianOfTouchingNeighbors(Image values, Image touch_matrix, Image median_values_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 values = clij2.push(valuesImagePlus);
ClearCLBuffer touch_matrix = clij2.push(touch_matrixImagePlus);
median_values_destination = clij2.create(values);

// Execute operation on GPU
clij2.medianOfTouchingNeighbors(values, touch_matrix, median_values_destination);

// show result
median_values_destinationImagePlus = clij2.pull(median_values_destination);
median_values_destinationImagePlus.show();

// cleanup memory on GPU
clij2.release(values);
clij2.release(touch_matrix);
clij2.release(median_values_destination);

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
values = clij2.pushMat(values_matrix);
touch_matrix = clij2.pushMat(touch_matrix_matrix);
median_values_destination = clij2.create(values);

% Execute operation on GPU
clij2.medianOfTouchingNeighbors(values, touch_matrix, median_values_destination);

% show result
median_values_destination = clij2.pullMat(median_values_destination)

% cleanup memory on GPU
clij2.release(values);
clij2.release(touch_matrix);
clij2.release(median_values_destination);

Icy JavaScript

// init CLIJ and GPU
importClass(net.haesleinhuepf.clicy.CLICY);
importClass(Packages.icy.main.Icy);

clij2 = CLICY.getInstance();

// get input parameters
values_sequence = getSequence();
values = clij2.pushSequence(values_sequence);
touch_matrix_sequence = getSequence();
touch_matrix = clij2.pushSequence(touch_matrix_sequence);
median_values_destination = clij2.create(values);

// Execute operation on GPU
clij2.medianOfTouchingNeighbors(values, touch_matrix, median_values_destination);

// show result
median_values_destination_sequence = clij2.pullSequence(median_values_destination)
Icy.addSequence(median_values_destination_sequence);
// cleanup memory on GPU
clij2.release(values);
clij2.release(touch_matrix);
clij2.release(median_values_destination);

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.median_of_touching_neighbors(values, touch_matrix, median_values_destination)

Example notebooks

filtering_in_graphs
neighbors_of_neighbors
tribolium_morphometry
neighbors_of_neighbors.ipynb
tissue_neighborhood_quantification.ipynb

Example scripts

filtering_in_graphs.ijm
neighbors_of_neighbors.ijm
tribolium_morphometry.ijm

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