GPU-accelerated image processing using cupy and CUDA

Related tags

Image Processingnapari-cupy-image-processing
Overview

napari-cupy-image-processing

License PyPI Python Version tests codecov

GPU-accelerated image processing using cupy and CUDA

img.png

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)

  • 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)

  • 0.2.1(Mar 20, 2022)

  • 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.
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  • 0.1.9(Jan 1, 2022)

  • 0.1.8(Dec 12, 2021)

  • 0.1.7(Dec 4, 2021)

    Backwards compatibible changes

    • Changed menu entries to cover finer differentiation between various filtering and segmentation techniquese
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  • 0.1.6(Nov 28, 2021)

  • 0.1.5(Nov 12, 2021)

  • 0.1.4(Nov 9, 2021)

  • 0.1.2(Oct 28, 2021)

  • 0.1.1(Oct 22, 2021)

  • 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
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Owner
Robert Haase
Computational Microscopist, BioImage Analyst, Code Jockey
Robert Haase
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