binaryFillHoles

Fills holes (pixels with value 0 surrounded by pixels with value 1) in a binary image.

Note: This function is known to perform slowly on large images. Consider using the extension CLIJx_morphoLibJFillHoles(input, destination) instead. Read more: http://clij.github.io/assistant/installation#extensions

Parameters

source : Image The binary input image where holes will be filled. destination : Image The output image where true pixels will be 1.

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.

binaryFillHoles often follows after

binaryFillHoles is often followed by

Usage in ImageJ macro

Ext.CLIJ2_binaryFillHoles(Image source, 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);
destination = clij2.create(source);

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

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

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

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

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

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

% show result
destination = clij2.pullMat(destination)

% cleanup memory on GPU
clij2.release(source);
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);
destination = clij2.create(source);

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

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

Example notebooks

binary_processing

Example scripts

benchmarkFillHoles.ijm
binary_processing.ijm
fillHoles.ijm

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