pyclesperanto 0.6.1

GPU-accelerated image processing in python using OpenCL

pyclesperanto

pyclesperanto is a python package for clEsperanto - a multi-language framework for GPU-accelerated image processing. clEsperanto uses OpenCL kernels from CLIJ. This package relies on the CLIc back-end for processing.

Usage

Note: This project is under heavy development. Functions and parameters are subject to change.

from skimage.io import imread
from pyclesperanto import cle

image = imread("https://imagej.nih.gov/ij/images/blobs.gif")

# push and create buffer
gpu_output = cle.create(image.shape)
gpu_input = cle.push(image)

# apply kernel
cle.add_image_and_scalar(input_image=gpu_input, output_image=gpu_output, scalar=100)

# visualize result
cle.imshow(gpu_output)

# get result as numpy array
result = cle.pull(gpu_output)

Example gallery

	Segment + analyze blobs
	Cell segmentation + Voronoi labeling
	3D image filtering
	Find local maxima
	3D Tribolium nuclei segmentation
	Explore application programming interface (API)

More usage and example can be found as notebooks in the user documentation folder

Installation

Download the repository and update the associated submodules:

git clone https://github.com/clEsperanto/pyclesperanto.git
cd pyclesperanto && git submodule update --init --recursive

Here, we assume that your system has an OpenCL valid device and that all its drivers are correctly installed. Using anaconda (or miniconda), create a virtual environment and activate it:

conda create --name pycle python=3.9
conda activate pycle

Finally, install pyclesperanto and all its dependencies by running the command:

pip install -e .

For MacOS users, Please install the following package:

conda install -c conda-forge -y ocl_icd_wrapper_apple

For Linux users, Please install the following package:

conda install -c conda-forge -y ocl-icd-system

Contributing

Contributions are very welcome. Before spending effort on coding and filing a pull-request, please get in touch, file an issue, and let's discuss your potential contribution.

License

Distributed under the terms of the BSD-3 license, "py-clesperanto" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.