convolve

Convolve the image with a given kernel image.

It is recommended that the kernel image has an odd size in X, Y and Z.

Category: Filter

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

convolve often follows after

create3D (1)

Usage in ImageJ macro

Ext.CLIJ2_convolve(Image source, Image convolution_kernel, 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 source = clij2.push(sourceImagePlus);
ClearCLBuffer convolution_kernel = clij2.push(convolution_kernelImagePlus);
destination = clij2.create(source);

// Execute operation on GPU
clij2.convolve(source, convolution_kernel, destination);

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

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

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
source = clij2.pushMat(source_matrix);
convolution_kernel = clij2.pushMat(convolution_kernel_matrix);
destination = clij2.create(source);

% Execute operation on GPU
clij2.convolve(source, convolution_kernel, destination);

% show result
destination = clij2.pullMat(destination)

% cleanup memory on GPU
clij2.release(source);
clij2.release(convolution_kernel);
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
source_sequence = getSequence();
source = clij2.pushSequence(source_sequence);
convolution_kernel_sequence = getSequence();
convolution_kernel = clij2.pushSequence(convolution_kernel_sequence);
destination = clij2.create(source);

// Execute operation on GPU
clij2.convolve(source, convolution_kernel, destination);

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

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.convolve(source, convolution_kernel, destination)

Example notebooks

benchmarking
benchmarking.ipynb
convolution.ipynb

Example scripts

benchmarking.ijm

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