# napari-cupy-image-processing
[](https://github.com/haesleinhuepf/napari-cupy-image-processing/raw/master/LICENSE)
[](https://pypi.org/project/napari-cupy-image-processing)
[](https://python.org)
[](https://github.com/haesleinhuepf/napari-cupy-image-processing/actions)
[](https://codecov.io/gh/haesleinhuepf/napari-cupy-image-processing)
[](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)
[](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.
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/
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"description": "# napari-cupy-image-processing\r\n\r\n[](https://github.com/haesleinhuepf/napari-cupy-image-processing/raw/master/LICENSE)\r\n[](https://pypi.org/project/napari-cupy-image-processing)\r\n[](https://python.org)\r\n[](https://github.com/haesleinhuepf/napari-cupy-image-processing/actions)\r\n[](https://codecov.io/gh/haesleinhuepf/napari-cupy-image-processing)\r\n[](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)\r\n[](https://napari-hub.org/plugins/napari-cupy-image-processing)\r\n\r\n\r\nGPU-accelerated image processing using [cupy](https://cupy.dev) and [CUDA](https://en.wikipedia.org/wiki/CUDA)\r\n\r\n## Usage\r\n\r\nThis napari plugin adds some menu entries to the Tools menu. You can recognize them with their suffix `(n-cupy)` in brackets.\r\nFurthermore, it can be used from the [napari-assistant](https://www.napari-hub.org/plugins/napari-assistant) graphical user interface. \r\nTherefore, just click the menu `Tools > Utilities > Assistant (na)` or run `naparia` from the command line.\r\n\r\n\r\n\r\nYou 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).\r\n\r\n## Installation\r\n\r\nYou can install `napari-cupy-image-processing` using conda:\r\n\r\n mamba install -c conda-forge cupy cudatoolkit=11.2 napari-cupy-image-processing\r\n\r\n## Troubleshooting installation\r\n\r\nIn case of issues, follow the [instructions for installing cupy](https://docs.cupy.dev/en/stable/install.html#installing-cupy-from-conda-forge). \r\n\r\nA more detailed example for installation (change 11.2 to your desired CUDA version):\r\n```\r\nmamba create --name cupy_p39 python=3.9 \r\nconda activate cupy_p39\r\n```\r\nAnd then:\r\n```\r\nmamba install -c conda-forge cupy cudatoolkit=11.2 napari-cupy-image-processing\r\n```\r\n\r\n## Contributing\r\n\r\nContributions 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 \r\n[implementation of the current operations](https://github.com/haesleinhuepf/napari-cupy-image-processing/blob/main/napari_cupy_image_processing/_cupy_image_processing.py#L48). \r\nIf you need another function in napari, just send a PR. Please make sure the tests pass locally before submitting a PR.\r\n\r\n```\r\npip install pytest-cov pytest-qt\r\npytest --cov=napari_cupy_image_processing\r\n```\r\n\r\nThis [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.\r\n\r\n## License\r\n\r\nDistributed under the terms of the [MIT] license,\r\n\"napari-cupy-image-processing\" is free and open source software\r\n\r\n## Issues\r\n\r\nIf you encounter any problems, please [file an issue] along with a detailed description.\r\n\r\n[napari]: https://github.com/napari/napari\r\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\r\n[@napari]: https://github.com/napari\r\n[MIT]: http://opensource.org/licenses/MIT\r\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\r\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\r\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\r\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\r\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\r\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\r\n\r\n[file an issue]: https://github.com/haesleinhuepf/napari-cupy-image-processing/issues\r\n\r\n[napari]: https://github.com/napari/napari\r\n[tox]: https://tox.readthedocs.io/en/latest/\r\n[pip]: https://pypi.org/project/pip/\r\n[PyPI]: https://pypi.org/\r\n",
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