minimum3DBox

Computes the local minimum of a pixels cube neighborhood.

The cubes size is specified by its half-width, half-height and half-depth (radius).

Category: Filter

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

minimum3DBox is often followed by

release (5)
maximum3DBox (1)

Usage in ImageJ macro

Ext.CLIJ2_minimum3DBox(Image source, Image destination, Number radius_x, Number radius_y, Number radius_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);
int radius_x = 10;
int radius_y = 20;
int radius_z = 30;

// Execute operation on GPU
clij2.minimum3DBox(source, destination, radius_x, radius_y, radius_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);
radius_x = 10;
radius_y = 20;
radius_z = 30;

% Execute operation on GPU
clij2.minimum3DBox(source, destination, radius_x, radius_y, radius_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);
radius_x = 10;
radius_y = 20;
radius_z = 30;

// Execute operation on GPU
clij2.minimum3DBox(source, destination, radius_x, radius_y, radius_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.minimum_box(source, destination, radius_x, radius_y, radius_z)

Example notebooks

segmentation_2d_membranes.ipynb

Example scripts

minimum.ijm
topHat.ijm

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