reference_connectedComponentsLabelingBox.md

connectedComponentsLabelingBox

Performs connected components analysis inspecting the box neighborhood of every pixel to a binary image and generates a label map.

Category: Labels

connectedComponentsLabelingBox often follows after

• automaticThreshold (1)
• minimum2DBox (1)
• binaryNot (4)
• openingBox (1)
• binaryFillHoles (2)
• closingBox (1)
• thresholdOtsu (4)
• binaryEdgeDetection (1)

connectedComponentsLabelingBox is often followed by

• extendLabelingViaVoronoi (1)
• replaceIntensities (2)
• maximumZProjection (1)
• excludeLabelsOnEdges (5)
• release (6)
• centroidsOfBackgroundAndLabels (1)
• maximum2DBox (1)
• getMaximumOfAllPixels (1)

Usage in ImageJ macro

Ext.CLIJ2_connectedComponentsLabelingBox(Image binary_input, Image labeling_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 binary_input = clij2.push(binary_inputImagePlus);
labeling_destination = clij2.create(binary_input);

// Execute operation on GPU
clij2.connectedComponentsLabelingBox(binary_input, labeling_destination);

// show result
labeling_destinationImagePlus = clij2.pull(labeling_destination);
labeling_destinationImagePlus.show();

// cleanup memory on GPU
clij2.release(binary_input);
clij2.release(labeling_destination);

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();
% get input parameters
binary_input = clij2.pushMat(binary_input_matrix);
labeling_destination = clij2.create(binary_input);

% Execute operation on GPU
clij2.connectedComponentsLabelingBox(binary_input, labeling_destination);

% show result
labeling_destination = clij2.pullMat(labeling_destination)

% cleanup memory on GPU
clij2.release(binary_input);
clij2.release(labeling_destination);

Icy JavaScript

// init CLIJ and GPU
importClass(net.haesleinhuepf.clicy.CLICY);
importClass(Packages.icy.main.Icy);
clij2 = CLICY.getInstance();
// get input parameters
binary_input_sequence = getSequence();
binary_input = clij2.pushSequence(binary_input_sequence);
labeling_destination = clij2.create(binary_input);

// Execute operation on GPU
clij2.connectedComponentsLabelingBox(binary_input, labeling_destination);

// show result
labeling_destination_sequence = clij2.pullSequence(labeling_destination)
Icy.addSequence(labeling_destination_sequence);
// cleanup memory on GPU
clij2.release(binary_input);
clij2.release(labeling_destination);

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle
cle.connected_components_labeling_box(binary_input, labeling_destination)

Example notebooks

labeling
labelmap_voronoi
mean_of_touching_neighbors
working_with_rois

Example scripts

division_visualisation.ijm
jaccard_matrix.ijm
labeling.ijm
labelmap_voronoi.ijm
mean_of_touching_neighbors.ijm
working_with_rois.ijm

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