https://github.com/yapic/napari-yapic-prediction
Image segmentation prediction tool that uses trained YAPiC model and performs image segmentation directly in Napari.
https://github.com/yapic/napari-yapic-prediction
napari-plugin
Last synced: 5 months ago
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Image segmentation prediction tool that uses trained YAPiC model and performs image segmentation directly in Napari.
- Host: GitHub
- URL: https://github.com/yapic/napari-yapic-prediction
- Owner: yapic
- License: gpl-3.0
- Created: 2021-04-16T08:40:07.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2022-09-19T07:58:31.000Z (almost 4 years ago)
- Last Synced: 2025-10-21T19:33:22.930Z (9 months ago)
- Topics: napari-plugin
- Language: Python
- Homepage: https://yapic.github.io/napari-yapic-prediction
- Size: 4.14 MB
- Stars: 0
- Watchers: 3
- Forks: 4
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# napari-yapic-prediction
[](https://github.com/yapic/napari-yapic-prediction/raw/master/LICENSE)
[](https://pypi.org/project/napari-yapic-prediction)
[](https://python.org)
[](https://github.com/yapic/napari-yapic-prediction/actions)
[](https://codecov.io/gh/yapic/napari-yapic-prediction)
A napari widget plugin to perform YAPiC model segmentation prediction in the napari window.
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This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.
## Description
This napari plugin provides a widget to upload a [YAPiC] trained model and perform segmentation over all the present images in the napari window. The segmentation results are uploaded as napari layers into the viewer automatically with the name structure of *imgename_prediction*.
## Installation
1. Please install either GPU or CPU version of tensorflow that is compatible with your `cuda` and `cudnn` libraries before installing the plugin depending on your system.
One of the plugin dependency is `yapic` that currently has sensitivity to tensorflow versions.
2. You can install `napari-yapic-prediction` via [pip]:
```pip install napari-yapic-prediction```
## Contributing
Contributions are very welcome. 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 [GNU GPL v3.0] license,
"napari-yapic-prediction" 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/yapic/napari-yapic-prediction/issues
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
[YAPiC]: https://yapic.github.io/yapic/