{"name":"napari-organoid-counter","display_name":"napari OrganoidCounter","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-organoid-counter.OrganoidCounterWidget","title":"Make organoid counter widget","python_name":"napari_organoid_counter._widget:OrganoidCounterWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-organoid-counter.get_reader","title":"Read \".json\" annotation files","python_name":"napari_organoid_counter._reader:get_reader","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-organoid-counter.get_reader","filename_patterns":["*.json"],"accepts_directories":false}],"writers":null,"widgets":[{"command":"napari-organoid-counter.OrganoidCounterWidget","display_name":"Organoid-Counter","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-organoid-counter","version":"0.2.3","dynamic":null,"platform":null,"supported_platform":null,"summary":"A plugin to automatically count lung organoids","description":"# Napari Organoid Counter - Version 0.2 is out! \n\n\n[](https://zenodo.org/badge/latestdoi/476715320)\n[](https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/raw/main/LICENSE)\n[](https://pypi.org/project/napari-organoid-counter)\n[](https://python.org)\n[](https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/actions)\n[](https://codecov.io/gh/HelmholtzAI-Consultants-Munich/napari-organoid-counter)\n[](https://napari-hub.org/plugins/napari-organoid-counter)\n\nA napari plugin to automatically count lung organoids from microscopy imaging data. *Note that this plugin only supports single channel grayscale images.*\n\n\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n\n## Installation\n\nYou can install `napari-organoid-counter` via [pip]:\n\n pip install napari-organoid-counter\n\n\nTo install latest development version :\n\n pip install git+https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter.git\n \n \nFor the dev branch you can clone this repo and install with:\n\n pip install -e . \n\nFor installing on a Windows machine via napari, follow the instuctions [here](https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/blob/main/readme-content/How%20to%20install%20on%20a%20Windows%20machine.pdf).\n\n## What's new in v2?\nCheckout our *What's New in v2* [here](https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/blob/main/.napari/DESCRIPTION.md#whats-new-in-v2).\n\n## How to use?\nAfter installing, you can start napari (either by typing ```napari``` in your terminal or by launching the application) and select the plugin from the drop down menu.\n\nFor more information on this plugin, its' intended audience, as well as Quickstart guide go to our [Quickstart guide](https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/blob/main/.napari/DESCRIPTION.md#quickstart).\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-organoid-counter\" is free and open source software\n\n## Dependencies\n\n\n```napari-organoid-counter``` uses the ```napari-aicsimageio```[1] [2] plugin for reading and processing CZI images.\n\n[1] Eva Maxfield Brown, Dan Toloudis, Jamie Sherman, Madison Swain-Bowden, Talley Lambert, AICSImageIO Contributors (2021). AICSImageIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub. https://github.com/AllenCellModeling/aicsimageio\n\n[2] Eva Maxfield Brown, Talley Lambert, Peter Sobolewski, Napari-AICSImageIO Contributors (2021). Napari-AICSImageIO: Image Reading in Napari using AICSImageIO [Computer software]. GitHub. https://github.com/AllenCellModeling/napari-aicsimageio\n\n## 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/HelmholtzAI-Consultants-Munich/napari-organoid-counter/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## Citing\n\nIf you use this plugin for your work, please cite it using the following:\n\n> Christina Bukas, Harshavardhan Subramanian, & Marie Piraud. (2023). HelmholtzAI-Consultants-Munich/napari-organoid-counter: v0.2.0 (v0.2.0). Zenodo. https://doi.org/10.5281/zenodo.7859571\n> \nbibtex:\n```\n@software{christina_bukas_2022_6457904,\n author = {Christina Bukas, Harshavardhan Subramanian, & Marie Piraud},\n title = {{HelmholtzAI-Consultants-Munich/napari-organoid- \n counter: second release of the napari plugin for lung\n organoid counting}},\n month = apr,\n year = 2023,\n publisher = {Zenodo},\n version = {v0.2.0},\n doi = {10.5281/zenodo.7859571},\n url = {https://doi.org/10.5281/zenodo.7859571}\n}\n```\n\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter","download_url":null,"author":"christinab12","author_email":"christina.bukas@helmholtz-muenchen.de","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 :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Operating System :: OS Independent","License :: OSI Approved :: MIT License"],"requires_dist":["napari[all] >=0.4.17","napari-aicsimageio >=0.7.2","torch >=1.13.1","torchvision >=0.14.1","tox ; extra == 'testing'","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'","pytest-qt ; extra == 'testing'","napari ; extra == 'testing'","pyqt5 ; extra == 'testing'"],"requires_python":"<3.11,>=3.8","requires_external":null,"project_url":["Bug Tracker, https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/issues","Documentation, https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter#README.md","Source Code, https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter","User Support, https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}