GPU-accelerated image processing using cupy and CUDA

Robert Haase

Last update: Oct 26, 2022

Related tags

Image Processing napari-cupy-image-processing

Overview

napari-cupy-image-processing

GPU-accelerated image processing using cupy and CUDA

This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-napari-plugin template.

Installation

Follow the instructions for installing cupy on your computer first. Afterwards, you can install napari-cupy-image-processing via pip:

pip install napari-cupy-image-processing

A more detailed example for installation (change 10.2 to your CUDA version):

conda create --name cupy_p38 python=3.8
conda activate cupy_p38
conda install -c conda-forge cupy cudatoolkit=10.2
conda install napari
pip install napari-cupy-image-processing

Known issues

When executing the first operation right after CUDA installation, napari may freeze and crash. Wait a minute and try again.

Contributing

Contributions are very welcome. Adding cupy ndimage functions is quite easy as you can see in the implementation of the current operations. If you need another function in napari, just send a PR. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the MIT license, "napari-cupy-image-processing" is free and open source software

Issues

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

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Releases(0.3.1)

0.3.1(Aug 27, 2022)
New features

nice display of image variables in jupyter notebooks

Source code(tar.gz)
Source code(zip)
0.3.0(Jul 10, 2022)
New features

Added docstrings to enable searching in them via the napari-assistant

Backwards compatibility breaking changes:

The unused viewer parameter of all functions was removed.

Deprecated methods:

The measurement() function has been deprecated because it was too slow and it will be removed with the next major release. Consider using napari-skimage-regionprops or napari-simpleitk-image-processing instead.

Source code(tar.gz)
Source code(zip)
0.2.3(May 8, 2022)
Deprecated functions

napari_cupy_image_processing.measurement() has been deprecated. Use napari_simpleitk_image_processing.label_statistics() instead.

Source code(tar.gz)
Source code(zip)
0.2.2(Mar 20, 2022)

Documentation update
Source code(tar.gz)
Source code(zip)
0.2.1(Mar 20, 2022)
New features

Added napari-assistant as graphical user interface

Source code(tar.gz)
Source code(zip)
0.2.0(Mar 8, 2022)
Bugfix:

measurements() was not easily callable from the API (Thanks to Edwin Hernandez G for reporting!)

Backwards compatibility breaking changes:

measurements() now takes images (numpy arrays) as parameters, and no longer napari layers.

Source code(tar.gz)
Source code(zip)
0.1.9(Jan 1, 2022)
New features

Measurements of labeled objects

Improvements

Tests (have to be executed locally. Github doesn't suppot GPUs)

Code coverage

Source code(tar.gz)
Source code(zip)
0.1.8(Dec 12, 2021)

Added __common_alias__ and simplified API for better code generation.
Source code(tar.gz)
Source code(zip)
0.1.7(Dec 4, 2021)
Backwards compatibible changes

Changed menu entries to cover finer differentiation between various filtering and segmentation techniquese

Source code(tar.gz)
Source code(zip)
0.1.6(Nov 28, 2021)
New features

Input images can be dask images now. They will be converted to numpy before passing over to the GPU

Source code(tar.gz)
Source code(zip)
0.1.5(Nov 12, 2021)
New features

use napari-time-slicer for processing timelapse data

Source code(tar.gz)
Source code(zip)
0.1.4(Nov 9, 2021)
New features

binary dilation

binary erosion

binary opening

binary closing

Source code(tar.gz)
Source code(zip)
0.1.2(Oct 28, 2021)
New features

Black top-hat filter

Minimum filter

Maximum filter

Shorter menu names

Source code(tar.gz)
Source code(zip)
0.1.1(Oct 22, 2021)

Improved documentation
Source code(tar.gz)
Source code(zip)
0.1.0(Oct 22, 2021)
New functions

gaussian_filter

gaussian_laplace

median_filter

percentile_filter

white_tophat

morphological_gradient

morphological_laplace

wiener

threshold_otsu

binary_fill_holes

label

Source code(tar.gz)
Source code(zip)

Owner

Robert Haase

Computational Microscopist, BioImage Analyst, Code Jockey

GitHub

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