CLIJ2
GPU accelerated image processing for everyone
maximumZProjection
Determines the maximum intensity projection of an image along Z.
Category: Projections
Availability: Available in Fiji by activating the update sites clij and clij2. This function is part of clij2_-2.5.0.1.jar.
maximumZProjection often follows after
- connectedComponentsLabelingBox (1)
- replaceIntensities (2)
- rotate3D (1)
- resliceLeft (1)
- onlyzeroOverwriteMaximumDiamond (1)
- resample (1)
maximumZProjection is often followed by
Usage in ImageJ macro
Ext.CLIJ2_maximumZProjection(Image source, Image destination_max);
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_max = clij2.create(new long[]{source.getWidth(), source.getHeight()}, source.getNativeType());
// Execute operation on GPU clij2.maximumZProjection(source, destination_max);
// show result destination_maxImagePlus = clij2.pull(destination_max); destination_maxImagePlus.show(); // cleanup memory on GPU clij2.release(source); clij2.release(destination_max);
Matlab
% init CLIJ and GPU clij2 = init_clatlab(); % get input parameters source = clij2.pushMat(source_matrix); destination_max = clij2.create([source.getWidth(), source.getHeight()], source.getNativeType());
% Execute operation on GPU clij2.maximumZProjection(source, destination_max);
% show result destination_max = clij2.pullMat(destination_max) % cleanup memory on GPU clij2.release(source); clij2.release(destination_max);
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_max = clij2.create([source.getWidth(), source.getHeight()], source.getNativeType());
// Execute operation on GPU clij2.maximumZProjection(source, destination_max);
// show result destination_max_sequence = clij2.pullSequence(destination_max) Icy.addSequence(destination_max_sequence); // cleanup memory on GPU clij2.release(source); clij2.release(destination_max);
clEsperanto Python (experimental)
import pyclesperanto_prototype as cle cle.maximum_z_projection(source, destination_max)
Example notebooks
basic_image_processing
drosophila_max_cylinder_projection
image_segmentation_3d
maximumProjection
process_multichannel_timelapse
superpixel_segmentation
tribolium_morphometry
inspecting_3d_images.ipynb
Segmentation_3D.ipynb
tribolium_morphometry.ipynb
intensity_projections.ipynb
Example scripts
basic_image_processing.ijm
bigImageTransfer.ijm
drosophila_max_cylinder_projection.ijm
image_segmentation_3d.ijm
maximumProjection.ijm
orthogonalMaximumProjections.ijm
process_5D_stack.ijm
process_multichannel_timelapse.ijm
rotating_sphere.ijm
superpixel_segmentation.ijm
tribolium_morphometry.ijm
maximumProjection.js
maximumProjection.groovy
maximumProjection.bsh
interactiveCylinderProjection.py
interactiveSphereProjection.py
multi_GPU_demo.py