{"name":"napari-DeepSpot","display_name":"napari-DeepSpot","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-DeepSpot.EnhanceSpot","title":"EnhanceSpot","python_name":"napari_deepspot._dock_widget:EnhanceSpot","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-DeepSpot.EnhanceSpot","display_name":"EnhanceSpot","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-DeepSpot","version":"0.0.7","dynamic":null,"platform":["UNKNOWN"],"supported_platform":null,"summary":"RNA spot enhancement for fluorescent microscopy images","description":"# napari-DeepSpot\n\n[![License](https://img.shields.io/pypi/l/napari-DeepSpot.svg?color=green)](https://github.com/ebouilhol/napari-DeepSpot/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-DeepSpot.svg?color=green)](https://pypi.org/project/napari-DeepSpot)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-DeepSpot.svg?color=green)](https://python.org)\n[![tests](https://github.com/ebouilhol/napari-DeepSpot/workflows/tests/badge.svg)](https://github.com/ebouilhol/napari-DeepSpot/actions)\n[![codecov](https://codecov.io/gh/ebouilhol/napari-DeepSpot/branch/main/graph/badge.svg)](https://codecov.io/gh/ebouilhol/napari-DeepSpot)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-DeepSpot)](https://napari-hub.org/plugins/napari-DeepSpot)\n\nRNA spot enhancement for fluorescent microscopy images.\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/docs/plugins/index.html\n-->\n\n## Installation\n\nYou can install `napari-DeepSpot` via [pip]:\n\n    pip install napari-DeepSpot\n\n## Build from source\n\nThis plugin is using Tensorflow, make sure your Python environment has Tensorflow, on create a new environment using the following commands:\n* Conda:  \n`conda env create -f environment.yml`  \n`conda activate deepspot-napari`\n* Or pip:   \n`pip install -r requirements.txt`\n\n## Usage\n\nOpen one or multiple images using Napari GUI : \nFile > Open > Select your image\n\nThe images are then displayed on Napari\n\nLoad the Plugin:\nPlugins > Napari-DeepSpot:Enhance Spot\n\n![Usage](./image/napari.png)\n\nClick on the right panel Button \"Enhance\"\n\nWait a few seconds for the magic to happen :\n\n![Usage](./image/napari_enhance.png)\n\nYou can see the original images and the enhanced version in the left panel in the layer section.\n\nTo save the images : File > Save all layers or File > Save selected layers.\n\n\n![Usage](./image/napari_video.gif)\n\n\n\n## Citation\nIf you use this plugin please cite the [paper](https://www.biorxiv.org/content/10.1101/2021.11.25.469984v1):\n\n>@article {Bouilhol2021DeepSpot,  \n>\t author = {Bouilhol, Emmanuel and Lefevre, Edgar and Dartigues, Benjamin and Brackin, Robyn and Savulescu, Anca Flavia and Nikolski, Macha},  \n>\t title = {DeepSpot: a deep neural network for RNA spot enhancement in smFISH microscopy images},  \n>\t elocation-id = {2021.11.25.469984},  \n>\t year = {2021},  \n>\t doi = {10.1101/2021.11.25.469984},  \n>\t publisher = {Cold Spring Harbor Laboratory},  \n>\t URL = {https://www.biorxiv.org/content/early/2021/11/25/2021.11.25.469984},  \n>\t eprint = {https://www.biorxiv.org/content/early/2021/11/25/2021.11.25.469984.full.pdf},  \n>\t journal = {bioRxiv}  \n>}  \n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [MIT] license,\n\"napari-DeepSpot\" is free and open source software\n\n## Known Issues\n\nIf you have troubles with the Python packages `typing extensions`, use the command :  \n`pip install typing-extensions --upgrade`  \n\nWhen using \"Enhance\" on multiple images, Napari may freeze. Just wait until it comes to life again, the images will still be enhanced. This is due to Napari memory usage and will be fix one day.\n\n\n## Other Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[file an issue]: https://github.com/ebouilhol/napari-DeepSpot/issues\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n\n\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/ebouilhol/napari-DeepSpot","download_url":null,"author":"Emmanuel Bouilhol","author_email":"emmanuel.bouilhol@u-bordeaux.fr","maintainer":null,"maintainer_email":null,"license":"MIT","classifier":["Development Status :: 2 - Pre-Alpha","Intended Audience :: Developers","Framework :: napari","Topic :: Software Development :: Testing","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3.7","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Operating System :: OS Independent","License :: OSI Approved :: MIT License"],"requires_dist":["napari-plugin-engine (>=0.1.4)","numpy","pytest","pytest-cov","pytest-xvfb","pytest-qt","napari","qtpy (==1.9.0)","pyqt5","tensorflow","scikit-image","opencv-python"],"requires_python":">=3.7","requires_external":null,"project_url":["Bug Tracker, https://github.com/ebouilhol/napari-DeepSpot/issues","Documentation, https://github.com/ebouilhol/napari-DeepSpot#README.md","Source Code, https://github.com/ebouilhol/napari-DeepSpot","User Support, https://github.com/ebouilhol/napari-DeepSpot/issues"],"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":true}