equalizeMeanIntensitiesOfSlices

Determines correction factors for each z-slice so that the average intensity in all slices can be made the same and multiplies these factors with the slices.

This functionality is similar to the ‘Simple Ratio Bleaching Correction’ in Fiji.

Categories: Filter, Math

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

equalizeMeanIntensitiesOfSlices often follows after

scale3D (1)

equalizeMeanIntensitiesOfSlices is often followed by

topHatBox (1)

Usage in ImageJ macro

Ext.CLIJ2_equalizeMeanIntensitiesOfSlices(Image input, Image destination, Number referenceSlice);

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 input = clij2.push(inputImagePlus);
destination = clij2.create(input);
int referenceSlice = 10;

// Execute operation on GPU
clij2.equalizeMeanIntensitiesOfSlices(input, destination, referenceSlice);

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

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

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
input = clij2.pushMat(input_matrix);
destination = clij2.create(input);
referenceSlice = 10;

% Execute operation on GPU
clij2.equalizeMeanIntensitiesOfSlices(input, destination, referenceSlice);

% show result
destination = clij2.pullMat(destination)

% cleanup memory on GPU
clij2.release(input);
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
input_sequence = getSequence();
input = clij2.pushSequence(input_sequence);
destination = clij2.create(input);
referenceSlice = 10;

// Execute operation on GPU
clij2.equalizeMeanIntensitiesOfSlices(input, destination, referenceSlice);

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

Example notebooks

image_segmentation_3d

Example scripts

image_segmentation_3d.ijm

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