CLIJ2
GPU accelerated image processing for everyone
copySlice
This method has two purposes: It copies a 2D image to a given slice z position in a 3D image stack or It copies a given slice at position z in an image stack to a 2D image.
The first case is only available via ImageJ macro. If you are using it, it is recommended that the target 3D image already pre-exists in GPU memory before calling this method. Otherwise, CLIJ create the image stack with z planes.
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.
copySlice often follows after
- replaceIntensities (2)
- affineTransform2D (2)
- maximumZProjection (2)
- rotate2D (2)
- binaryFillHoles (1)
- scale2D (1)
- translate2D (1)
- applyVectorField2D (1)
- flip2D (1)
- mask (2)
copySlice is often followed by
- histogram (2)
- gaussianBlur2D (1)
- affineTransform2D (2)
- binaryFillHoles (1)
- release (1)
- statisticsOfBackgroundAndLabelledPixels (2)
- thresholdOtsu (1)
- crop3D (1)
- differenceOfGaussian2D (1)
- statisticsOfLabelledPixels (1)
Usage in ImageJ macro
Ext.CLIJ2_copySlice(Image source, Image destination, Number slice_index);
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(new long[]{source.getWidth(), source.getHeight()}, source.getNativeType());
int slice_index = 10;
// Execute operation on GPU clij2.copySlice(source, destination, slice_index);
// 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.getWidth(), source.getHeight()], source.getNativeType()); slice_index = 10;
% Execute operation on GPU clij2.copySlice(source, destination, slice_index);
% 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.getWidth(), source.getHeight()], source.getNativeType()); slice_index = 10;
// Execute operation on GPU clij2.copySlice(source, destination, slice_index);
// 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.copy_slice(source, destination, slice_index)
Example notebooks
basic_image_processing
inspecting_3d_images.ipynb
Segmentation_3D.ipynb
voronoi_otsu_labeling.ipynb
benchmarking_centroids_of_labels.ipynb
statistics_of_labeled_pixels.ipynb
Example scripts
allocateBigImages.ijm
applyVectorField.ijm
basic_image_processing.ijm
division_visualisation.ijm
motionCorrection.ijm
motionCorrection_compare_stackreg.ijm
process_5D_stack.ijm
rotateFree.ijm
rotateOverwriteOriginal.ijm
rotating_sphere.ijm
scaleFree.ijm
translate.ijm
tubeness.ijm
applyVectorField.py
rotateFree.py
rotateOverwriteOiginal.py