neighborsOfNeighbors

Determines neighbors of neigbors from touch matrix and saves the result as a new touch matrix.

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

neighborsOfNeighbors often follows after

generateTouchMatrix (2)

neighborsOfNeighbors is often followed by

meanOfTouchingNeighbors (2)

Usage in ImageJ macro

Ext.CLIJ2_neighborsOfNeighbors(Image touch_matrix, Image neighbor_matrix_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 touch_matrix = clij2.push(touch_matrixImagePlus);
neighbor_matrix_destination = clij2.create(touch_matrix);

// Execute operation on GPU
clij2.neighborsOfNeighbors(touch_matrix, neighbor_matrix_destination);

// show result
neighbor_matrix_destinationImagePlus = clij2.pull(neighbor_matrix_destination);
neighbor_matrix_destinationImagePlus.show();

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

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
touch_matrix = clij2.pushMat(touch_matrix_matrix);
neighbor_matrix_destination = clij2.create(touch_matrix);

% Execute operation on GPU
clij2.neighborsOfNeighbors(touch_matrix, neighbor_matrix_destination);

% show result
neighbor_matrix_destination = clij2.pullMat(neighbor_matrix_destination)

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

Icy JavaScript

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

clij2 = CLICY.getInstance();

// get input parameters
touch_matrix_sequence = getSequence();
touch_matrix = clij2.pushSequence(touch_matrix_sequence);
neighbor_matrix_destination = clij2.create(touch_matrix);

// Execute operation on GPU
clij2.neighborsOfNeighbors(touch_matrix, neighbor_matrix_destination);

// show result
neighbor_matrix_destination_sequence = clij2.pullSequence(neighbor_matrix_destination)
Icy.addSequence(neighbor_matrix_destination_sequence);
// cleanup memory on GPU
clij2.release(touch_matrix);
clij2.release(neighbor_matrix_destination);

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.neighbors_of_neighbors(touch_matrix, neighbor_matrix_destination)

Example notebooks

neighbors_of_neighbors
neighbors_of_neighbors.ipynb

Example scripts

neighbors_of_neighbors.ijm

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