topHatBox

Applies a top-hat filter for background subtraction to the input image.

Parameters

input : Image The input image where the background is subtracted from. destination : Image The output image where results are written into. radius_x : Image Radius of the background determination region in X. radius_y : Image Radius of the background determination region in Y. radius_z : Image Radius of the background determination region in Z.

Categories: Filter, Background

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

topHatBox often follows after

topHatBox is often followed by

Usage in ImageJ macro

Ext.CLIJ2_topHatBox(Image input, Image destination, Number radiusX, Number radiusY, Number radiusZ);

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 radiusX = 10;
int radiusY = 20;
int radiusZ = 30;

// Execute operation on GPU
clij2.topHatBox(input, destination, radiusX, radiusY, radiusZ);

// 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);
radiusX = 10;
radiusY = 20;
radiusZ = 30;

% Execute operation on GPU
clij2.topHatBox(input, destination, radiusX, radiusY, radiusZ);

% 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);
radiusX = 10;
radiusY = 20;
radiusZ = 30;

// Execute operation on GPU
clij2.topHatBox(input, destination, radiusX, radiusY, radiusZ);

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

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.top_hat_box(input, destination, radius_x, radius_y, radius_z)

Example notebooks

compare_workflows
custom_clij_macro_functions
image_segmentation_3d
time_tracing
Segmentation_3D.ipynb

Example scripts

compare_workflows.ijm
custom_clij_macro_functions.ijm
image_segmentation_3d.ijm
time_tracing.ijm
napari_performance_demo.py

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