generateTouchMatrix

Takes a labelmap with n labels and generates a (n+1)*(n+1) matrix where all pixels are set to 0 exept those where labels are touching.

Only half of the matrix is filled (with x < y). For example, if labels 3 and 4 are touching then the pixel (3,4) in the matrix will be set to 1. The touch matrix is a representation of a region adjacency graph

Categories: Graphs, Measurements, Labels

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

generateTouchMatrix often follows after

generateTouchMatrix is often followed by

standardDeviationOfTouchingNeighbors (2)
minimumOfTouchingNeighbors (2)
countTouchingNeighbors (1)
release (4)
neighborsOfNeighbors (2)
medianOfTouchingNeighbors (2)
meanOfTouchingNeighbors (1)
touchMatrixToMesh (7)
multiplyImages (1)
maximumOfTouchingNeighbors (2)
averageDistanceOfTouchingNeighbors (1)

Usage in ImageJ macro

Ext.CLIJ2_generateTouchMatrix(Image label_map, Image touch_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 label_map = clij2.push(label_mapImagePlus);
touch_matrix_destination = clij2.create(label_map);

// Execute operation on GPU
clij2.generateTouchMatrix(label_map, touch_matrix_destination);

// show result
touch_matrix_destinationImagePlus = clij2.pull(touch_matrix_destination);
touch_matrix_destinationImagePlus.show();

// cleanup memory on GPU
clij2.release(label_map);
clij2.release(touch_matrix_destination);

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
label_map = clij2.pushMat(label_map_matrix);
touch_matrix_destination = clij2.create(label_map);

% Execute operation on GPU
clij2.generateTouchMatrix(label_map, touch_matrix_destination);

% show result
touch_matrix_destination = clij2.pullMat(touch_matrix_destination)

% cleanup memory on GPU
clij2.release(label_map);
clij2.release(touch_matrix_destination);

Icy JavaScript

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

clij2 = CLICY.getInstance();

// get input parameters
label_map_sequence = getSequence();
label_map = clij2.pushSequence(label_map_sequence);
touch_matrix_destination = clij2.create(label_map);

// Execute operation on GPU
clij2.generateTouchMatrix(label_map, touch_matrix_destination);

// show result
touch_matrix_destination_sequence = clij2.pullSequence(touch_matrix_destination)
Icy.addSequence(touch_matrix_destination_sequence);
// cleanup memory on GPU
clij2.release(label_map);
clij2.release(touch_matrix_destination);

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.generate_touch_matrix(label_map, touch_matrix_destination)

Example notebooks

filtering_in_graphs
mean_of_touching_neighbors
neighbors_of_neighbors
spots_pointlists_matrices_tables
superpixel_segmentation
tribolium_morphometry
spots_pointlists_matrices_tables.ipynb
mesh_between_touching_neighbors.ipynb
mesh_with_distances.ipynb
neighbors_of_neighbors.ipynb
shape_descriptors_based_on_neighborhood_graphs.ipynb
tissue_neighborhood_quantification.ipynb
tribolium_morphometry.ipynb

Example scripts

division_visualisation.ijm
filtering_in_graphs.ijm
large_matrices.ijm
mean_of_touching_neighbors.ijm
meshTouchingNeighbors.ijm
neighbors_of_neighbors.ijm
rotating_sphere.ijm
spots_pointlists_matrices_tables.ijm
superpixel_segmentation.ijm
tribolium_morphometry.ijm
mesh_close_points.m

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