https://github.com/haesleinhuepf/napari-cupy-image-processing

https://github.com/haesleinhuepf/napari-cupy-image-processing

napari-plugin

Last synced: 7 days ago
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• Host: GitHub
• URL: https://github.com/haesleinhuepf/napari-cupy-image-processing
• Owner: haesleinhuepf
• License: mit
• Created: 2021-10-22T18:39:45.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2023-08-17T12:36:00.000Z (over 1 year ago)
• Last Synced: 2025-04-14T08:45:00.377Z (23 days ago)
• Topics: napari-plugin
• Language: Python
• Homepage:
• Size: 10.3 MB
• Stars: 22
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# napari-cupy-image-processing

[![License](https://img.shields.io/pypi/l/napari-cupy-image-processing.svg?color=green)](https://github.com/haesleinhuepf/napari-cupy-image-processing/raw/master/LICENSE)

[![PyPI](https://img.shields.io/pypi/v/napari-cupy-image-processing.svg?color=green)](https://pypi.org/project/napari-cupy-image-processing)

[![Python Version](https://img.shields.io/pypi/pyversions/napari-cupy-image-processing.svg?color=green)](https://python.org)

[![tests](https://github.com/haesleinhuepf/napari-cupy-image-processing/workflows/tests/badge.svg)](https://github.com/haesleinhuepf/napari-cupy-image-processing/actions)

[![codecov](https://codecov.io/gh/haesleinhuepf/napari-cupy-image-processing/branch/master/graph/badge.svg)](https://codecov.io/gh/haesleinhuepf/napari-cupy-image-processing)

[![Development Status](https://img.shields.io/pypi/status/napari-cupy-image-processing.svg)](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)

[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-cupy-image-processing)](https://napari-hub.org/plugins/napari-cupy-image-processing)

GPU-accelerated image processing using [cupy](https://cupy.dev) and [CUDA](https://en.wikipedia.org/wiki/CUDA)

## Usage

This napari plugin adds some menu entries to the Tools menu. You can recognize them with their suffix `(n-cupy)` in brackets.

Furthermore, it can be used from the [napari-assistant](https://www.napari-hub.org/plugins/napari-assistant) graphical user interface. 

Therefore, just click the menu `Tools > Utilities > Assistant (na)` or run `naparia` from the command line.

![img.png](https://github.com/haesleinhuepf/napari-cupy-image-processing/raw/main/docs/screenshot-with-tools-menu.png)

You can also call operations from python, e.g. as shown in this [demo notebook](https://github.com/haesleinhuepf/napari-cupy-image-processing/raw/main/docs/demo.ipynb).

## Installation

You can install `napari-cupy-image-processing` using conda:

    mamba install -c conda-forge cupy cudatoolkit=11.2 napari-cupy-image-processing

## Troubleshooting installation

In case of issues, follow the [instructions for installing cupy](https://docs.cupy.dev/en/stable/install.html#installing-cupy-from-conda-forge). 

A more detailed example for installation (change 11.2 to your desired CUDA version):

```

mamba create --name cupy_p39 python=3.9 

conda activate cupy_p39

```

And then:

```

mamba install -c conda-forge cupy cudatoolkit=11.2 napari-cupy-image-processing

```

## Contributing

Contributions are very welcome. Adding [cupy ndimage](https://docs.cupy.dev/en/stable/reference/ndimage.html) functions is quite easy as you can see in the 

[implementation of the current operations](https://github.com/haesleinhuepf/napari-cupy-image-processing/blob/main/napari_cupy_image_processing/_cupy_image_processing.py#L48). 

If you need another function in napari, just send a PR. Please make sure the tests pass locally before submitting a PR.

```

pip install pytest-cov pytest-qt

pytest --cov=napari_cupy_image_processing

```

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

## 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.

[napari]: https://github.com/napari/napari

[Cookiecutter]: https://github.com/audreyr/cookiecutter

[@napari]: https://github.com/napari

[MIT]: http://opensource.org/licenses/MIT

[BSD-3]: http://opensource.org/licenses/BSD-3-Clause

[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt

[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt

[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0

[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt

[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin

[file an issue]: https://github.com/haesleinhuepf/napari-cupy-image-processing/issues

[napari]: https://github.com/napari/napari

[tox]: https://tox.readthedocs.io/en/latest/

[pip]: https://pypi.org/project/pip/

[PyPI]: https://pypi.org/