mask

Computes a masked image by applying a binary mask to an image.

All pixel values x of image X will be copied to the destination image in case pixel value m at the same position in the mask image is not equal to zero.

f(x,m) = (x if (m != 0); (0 otherwise))

Categories: Filter, Binary

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

mask often follows after

mask is often followed by

Usage in ImageJ macro

Ext.CLIJ2_mask(Image source, Image mask, 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 mask = clij2.push(maskImagePlus);
destination = clij2.create(source);

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

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

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

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
source = clij2.pushMat(source_matrix);
mask = clij2.pushMat(mask_matrix);
destination = clij2.create(source);

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

% show result
destination = clij2.pullMat(destination)

% cleanup memory on GPU
clij2.release(source);
clij2.release(mask);
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);
mask_sequence = getSequence();
mask = clij2.pushSequence(mask_sequence);
destination = clij2.create(source);

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

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

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.mask(source, mask, destination)

Example notebooks

outlines_numbers_overlay
tribolium_morphometry
voronoi_otsu_labeling
napari_dask.ipynb
voronoi_otsu_labeling.ipynb
tribolium_morphometry.ipynb

Example scripts

division_visualisation.ijm
intensity_per_label.ijm
outlines_numbers_overlay.ijm
tribolium_morphometry.ijm
voronoi_otsu_labeling.ijm
statistics.py
tribolium.py

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