driftCorrectionByCentroidFixation

Threshold the image stack, determines the centroid of the resulting binary image and translates the image stack so that its centroid sits in a defined position.

Category: Transformations

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_driftCorrectionByCentroidFixation(Image input, Image destination, Number relative_center_x, Number relative_center_y, Number relative_center_z, Number threshold);

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 input = clijx.push(inputImagePlus);
destination = clijx.create(input);
float relative_center_x = 1.0;
float relative_center_y = 2.0;
float relative_center_z = 3.0;
float threshold = 4.0;

// Execute operation on GPU
clijx.driftCorrectionByCentroidFixation(input, destination, relative_center_x, relative_center_y, relative_center_z, threshold);

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

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

Matlab

% init CLIJ and GPU
clijx = init_clatlabx();

% get input parameters
input = clijx.pushMat(input_matrix);
destination = clijx.create(input);
relative_center_x = 1.0;
relative_center_y = 2.0;
relative_center_z = 3.0;
threshold = 4.0;

% Execute operation on GPU
clijx.driftCorrectionByCentroidFixation(input, destination, relative_center_x, relative_center_y, relative_center_z, threshold);

% show result
destination = clijx.pullMat(destination)

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

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