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 clij2_-2.5.0.1.jar.

Usage in ImageJ macro

Ext.CLIJ2_drawDistanceMeshBetweenTouchingLabels(Image input, Image 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 input = clij2.push(inputImagePlus);
destination = clij2.create(input);

// Execute operation on GPU
clij2.drawDistanceMeshBetweenTouchingLabels(input, destination);

// show result
destinationImagePlus = clij2.pull(destination);
destinationImagePlus.show();

// cleanup memory on GPU
clij2.release(input);
clij2.release(destination);

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
input = clij2.pushMat(input_matrix);
destination = clij2.create(input);

% Execute operation on GPU
clij2.drawDistanceMeshBetweenTouchingLabels(input, destination);

% show result
destination = clij2.pullMat(destination)

% cleanup memory on GPU
clij2.release(input);
clij2.release(destination);

Icy JavaScript

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

clij2 = CLICY.getInstance();

// get input parameters
input_sequence = getSequence();
input = clij2.pushSequence(input_sequence);
destination = clij2.create(input);

// Execute operation on GPU
clij2.drawDistanceMeshBetweenTouchingLabels(input, destination);

// show result
destination_sequence = clij2.pullSequence(destination)
Icy.addSequence(destination_sequence);
// cleanup memory on GPU
clij2.release(input);
clij2.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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