colorDeconvolution

By Peter Haub

Computes the color deconvolution of an 8bit RGB stack color image with a given 3x3 matrix of color vectors. Note: The input image has to be a stack with three z-slices corresponding to the red, green and blue channel.)

Additional information see Supplementary Information to:

Haub, P., Meckel, T. A Model based Survey of Colour Deconvolution in Diagnostic Brightfield Microscopy: Error Estimation and Spectral Consideration. Sci Rep 5, 12096 (2015). https://doi.org/10.1038/srep12096

Category: Filter

Availability: Available in Fiji by activating the update sites clij and clij2. This function is part of clijx_-0.32.0.1.jar.

Usage in ImageJ macro

Ext.CLIJx_colorDeconvolution(Image source, Image color_vectors, Image destination);

Usage in object oriented programming languages

Java

// init CLIJ and GPU
import net.haesleinhuepf.clijx.CLIJx;
import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
CLIJx clijx = CLIJx.getInstance();

// get input parameters
ClearCLBuffer source = clijx.push(sourceImagePlus);
ClearCLBuffer color_vectors = clijx.push(color_vectorsImagePlus);
destination = clijx.create(source);

// Execute operation on GPU
clijx.colorDeconvolution(source, color_vectors, destination);

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

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

Matlab

% init CLIJ and GPU
clijx = init_clatlabx();

% get input parameters
source = clijx.pushMat(source_matrix);
color_vectors = clijx.pushMat(color_vectors_matrix);
destination = clijx.create(source);

% Execute operation on GPU
clijx.colorDeconvolution(source, color_vectors, destination);

% show result
destination = clijx.pullMat(destination)

% cleanup memory on GPU
clijx.release(source);
clijx.release(color_vectors);
clijx.release(destination);

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