drawDistanceMeshBetweenTouchingLabels

Starting from a label map, draw lines between touching neighbors resulting in a mesh.

The end points of the lines correspond to the centroids of the labels. The intensity of the lines corresponds to the distance between these labels (in pixels or voxels).

Categories: Graphs, Labels, Measurements

Availability: Available in Fiji by activating the update sites clij and clij2. This function is part of clijx_-0.30.1.22.jar.

Usage in ImageJ macro

Ext.CLIJx_drawDistanceMeshBetweenTouchingLabels(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.drawDistanceMeshBetweenTouchingLabels(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.drawDistanceMeshBetweenTouchingLabels(input, destination);

% show result
destination = clijx.pullMat(destination)

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

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.draw_distance_mesh_between_touching_labels(input, destination)

Example notebooks

mesh_with_distances.ipynb
shape_descriptors_based_on_neighborhood_graphs.ipynb

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