Metadata-Version: 2.1
Name: napari-ufish
Version: 0.0.3
Summary: Deep learning-based FISH spot calling method.
Author: Weize Xu
Author-email: vet.xwz@gmail.com
License: MIT
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: magicgui
Requires-Dist: qtpy
Requires-Dist: scikit-image
Requires-Dist: ufish
Requires-Dist: napari
Provides-Extra: testing
Requires-Dist: tox ; extra == 'testing'
Requires-Dist: pytest ; extra == 'testing'
Requires-Dist: pytest-cov ; extra == 'testing'
Requires-Dist: pytest-qt ; extra == 'testing'
Requires-Dist: pyqt5 ; extra == 'testing'

# napari-ufish

[![License MIT](https://img.shields.io/pypi/l/napari-ufish.svg?color=green)](https://github.com/UFISH-Team/napari-ufish/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/napari-ufish.svg?color=green)](https://pypi.org/project/napari-ufish)
[![Python Version](https://img.shields.io/pypi/pyversions/napari-ufish.svg?color=green)](https://python.org)
[![tests](https://github.com/UFISH-Team/napari-ufish/workflows/tests/badge.svg)](https://github.com/UFISH-Team/napari-ufish/actions)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-ufish)](https://napari-hub.org/plugins/napari-ufish)

Deep learning-based FISH spot calling method.
The napari plugin for [U-FISH](https://github.com/UFISH-Team/U-FISH).

## Links

+ [U-FISH](https://github.com/UFISH-Team/U-FISH)
+ [U-FISH models](https://huggingface.co/GangCaoLab/U-FISH)
+ [FISH_spots dataset](https://huggingface.co/datasets/GangCaoLab/FISH_spots)

## TODO List

- [x] Sample image
- [x] Inference interface
    - [x] Inference parameters
    - [x] Load model from path
    - [x] Help information dialog
- [x] Training interface

----------------------------------

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

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Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started

and review the napari docs for plugin developers:
https://napari.org/stable/plugins/index.html
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## Installation

You can install `napari-ufish` via [pip]:

    pip install napari-ufish


## 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 [MIT] license,
"napari-ufish" 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

[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
