jaccardIndex

Determines the overlap of two binary images using the Jaccard index.

A value of 0 suggests no overlap, 1 means perfect overlap. The resulting Jaccard index is saved to the results table in the ‘Jaccard_Index’ column. Note that the Sorensen-Dice coefficient can be calculated from the Jaccard index j using this formula:

s = f(j) = 2 j / (j + 1)

Categories: Measurements, Binary

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_jaccardIndex(Image source1, Image source2);

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 source1 = clij2.push(source1ImagePlus);
ClearCLBuffer source2 = clij2.push(source2ImagePlus);

// Execute operation on GPU
double resultJaccardIndex = clij2.jaccardIndex(source1, source2);

// show result
System.out.println(resultJaccardIndex);

// cleanup memory on GPU
clij2.release(source1);
clij2.release(source2);

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
source1 = clij2.pushMat(source1_matrix);
source2 = clij2.pushMat(source2_matrix);

% Execute operation on GPU
double resultJaccardIndex = clij2.jaccardIndex(source1, source2);

% show result
System.out.println(resultJaccardIndex);

% cleanup memory on GPU
clij2.release(source1);
clij2.release(source2);

Icy JavaScript

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

clij2 = CLICY.getInstance();

// get input parameters
source1_sequence = getSequence();
source1 = clij2.pushSequence(source1_sequence);
source2_sequence = getSequence();
source2 = clij2.pushSequence(source2_sequence);

// Execute operation on GPU
double resultJaccardIndex = clij2.jaccardIndex(source1, source2);

// show result
System.out.println(resultJaccardIndex);

// cleanup memory on GPU
clij2.release(source1);
clij2.release(source2);

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.jaccard_index(source1, source2)

Example scripts

jaccardIndex.py

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