Metadata-Version: 2.1
Name: napari-DeepSpot
Version: 0.0.1
Summary: RNA spot enhancement for fluorescent microscopy images
Home-page: https://github.com/ebouilhol/napari-DeepSpot
Author: Emmanuel Bouilhol
Author-email: emmanuel.bouilhol@u-bordeaux.fr
License: MIT
Project-URL: Bug Tracker, https://github.com/ebouilhol/napari-DeepSpot/issues
Project-URL: Documentation, https://github.com/ebouilhol/napari-DeepSpot#README.md
Project-URL: Source Code, https://github.com/ebouilhol/napari-DeepSpot
Project-URL: User Support, https://github.com/ebouilhol/napari-DeepSpot/issues
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Framework :: napari
Classifier: Topic :: Software Development :: Testing
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE

# napari-DeepSpot

[![License](https://img.shields.io/pypi/l/napari-DeepSpot.svg?color=green)](https://github.com/ebouilhol/napari-DeepSpot/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/napari-DeepSpot.svg?color=green)](https://pypi.org/project/napari-DeepSpot)
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[![tests](https://github.com/ebouilhol/napari-DeepSpot/workflows/tests/badge.svg)](https://github.com/ebouilhol/napari-DeepSpot/actions)
[![codecov](https://codecov.io/gh/ebouilhol/napari-DeepSpot/branch/main/graph/badge.svg)](https://codecov.io/gh/ebouilhol/napari-DeepSpot)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-DeepSpot)](https://napari-hub.org/plugins/napari-DeepSpot)

RNA spot enhancement for fluorescent microscopy images.

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

<!--
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/docs/plugins/index.html
-->

## Installation

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

    pip install napari-DeepSpot

## Python environment

This plugin is using Tensorflow, make sure your Python environment has Tensorflow, on create a new environment using the following commands:
* Conda:  
`conda env create -f environment.yml`  
`conda activate deepspot-napari`
* Or pip:   
`pip install -r requirements.txt`

## Usage

Open one or multiple images using Napari GUI : 
File > Open > Select your image

The images are then displayed on Napari

Load the Plugin:
Plugins > Napari-DeepSpot:Enhance Spot

![Usage](./image/napari.png)

Click on the right panel Button "Enhance"

Wait a few seconds for the magic to happen :

![Usage](./image/napari_enhance.png)

You can see the original images and the enhanced version in the left panel in the layer section.

To save the images : File > Save all layers or File > Save selected layers.

## Known Issues

If you have troubles with the Python packages `typing extensions`, use the command :  
`pip install typing-extensions --upgrade`  

When using "Enhance" on multiple images, Napari may freeze. Just wait until it comes to live again, the images will still be enhanced.


## Citation
If you use this plugin please cite the [paper](https://www.biorxiv.org/content/10.1101/2021.11.25.469984v1):

>@article {Bouilhol2021DeepSpot,  
>	 author = {Bouilhol, Emmanuel and Lefevre, Edgar and Dartigues, Benjamin and Brackin, Robyn and Savulescu, Anca Flavia and Nikolski, Macha},  
>	 title = {DeepSpot: a deep neural network for RNA spot enhancement in smFISH microscopy images},  
>	 elocation-id = {2021.11.25.469984},  
>	 year = {2021},  
>	 doi = {10.1101/2021.11.25.469984},  
>	 publisher = {Cold Spring Harbor Laboratory},  
>	 URL = {https://www.biorxiv.org/content/early/2021/11/25/2021.11.25.469984},  
>	 eprint = {https://www.biorxiv.org/content/early/2021/11/25/2021.11.25.469984.full.pdf},  
>	 journal = {bioRxiv}  
>}  

## 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-DeepSpot" 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/ebouilhol/napari-DeepSpot/issues

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


