rotate3D

Rotates an image stack in 3D.

All angles are entered in degrees. If the image is not rotated around the center, it is rotated around the coordinate origin.

It is recommended to apply the rotation to an isotropic image stack.

Category: Transformations

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

rotate3D often follows after

transposeXY (2)
touchMatrixToMesh (1)

rotate3D is often followed by

maximumZProjection (1)
topHatBox (1)

Usage in ImageJ macro

Ext.CLIJ2_rotate3D(Image source, Image destination, Number angleX, Number angleY, Number angleZ, Boolean rotateAroundCenter);

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 angleX = 1.0;
float angleY = 2.0;
float angleZ = 3.0;
boolean rotateAroundCenter = true;

// Execute operation on GPU
clij2.rotate3D(source, destination, angleX, angleY, angleZ, rotateAroundCenter);

// 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);
angleX = 1.0;
angleY = 2.0;
angleZ = 3.0;
rotateAroundCenter = true;

% Execute operation on GPU
clij2.rotate3D(source, destination, angleX, angleY, angleZ, rotateAroundCenter);

% 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);
angleX = 1.0;
angleY = 2.0;
angleZ = 3.0;
rotateAroundCenter = true;

// Execute operation on GPU
clij2.rotate3D(source, destination, angleX, angleY, angleZ, rotateAroundCenter);

// 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.rotate(source, destination, angleX, angleY, angleZ, rotateAroundCenter)

Example notebooks

affine_transforms.ipynb

Example scripts

rotating_sphere.ijm

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