gaussianBlur3D

Computes the Gaussian blurred image of an image given two sigma values in X, Y and Z.

Thus, the filterkernel can have non-isotropic shape.

The implementation is done separable. In case a sigma equals zero, the direction is not blurred.

Categories: Noise, Filter

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

gaussianBlur3D is often followed by

Usage in ImageJ macro

Ext.CLIJ2_gaussianBlur3D(Image source, Image destination, Number sigma_x, Number sigma_y, Number sigma_z);

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);
float sigma_x = 1.0;
float sigma_y = 2.0;
float sigma_z = 3.0;

// Execute operation on GPU
clij2.gaussianBlur3D(source, destination, sigma_x, sigma_y, sigma_z);

// 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);
sigma_x = 1.0;
sigma_y = 2.0;
sigma_z = 3.0;

% Execute operation on GPU
clij2.gaussianBlur3D(source, destination, sigma_x, sigma_y, sigma_z);

% 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);
sigma_x = 1.0;
sigma_y = 2.0;
sigma_z = 3.0;

// Execute operation on GPU
clij2.gaussianBlur3D(source, destination, sigma_x, sigma_y, sigma_z);

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

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.gaussian_blur(source, destination, sigma_x, sigma_y, sigma_z)

Example notebooks

basic_image_processing
blur
tribolium_morphometry
count_blobs.ipynb
napari_dask.ipynb
bead_segmentation.ipynb
voronoi_otsu_labeling.ipynb
tribolium_morphometry.ipynb
benchmarking_some_operations.ipynb
gaussian_blur.ipynb

Example scripts

backgroundSubtraction.ijm
basic_image_processing.ijm
blur.ijm
meshTouchingNeighbors.ijm
tribolium_morphometry.ijm
tubeness.ijm
blur_frame_by_frame.js
count_blobs.py
napari_.py
napari_magicgui.py
tribolium.py

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