{"name":"napari-organoid-counter","display_name":"napari organoid counter","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","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","*.json.draft"],"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":"2.4","name":"napari-organoid-counter","version":"0.2.9","dynamic":["author","author-email","classifier","description","description-content-type","home-page","license","license-file","project-url","provides-extra","requires-dist","requires-python","summary"],"platform":null,"supported_platform":null,"summary":"A plugin to automatically count lung organoids using Deep Learning.","description":"# Napari Organoid Counter - Version 0.2.9 is out! \n\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-organoid-counter)](https://napari-hub.org/plugins/napari-organoid-counter)\n![stability-stable](https://img.shields.io/badge/stability-stable-green.svg)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6457903.svg)](https://doi.org/10.5281/zenodo.6457903)\n[![License](https://img.shields.io/pypi/l/napari-organoid-counter.svg?color=green)](https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-organoid-counter.svg?color=green)](https://pypi.org/project/napari-organoid-counter)\n[![Python Version](https://img.shields.io/badge/python-3.11-blue)](https://python.org)\n[![tests](https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/workflows/tests/badge.svg)](https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/actions)\n[![codecov](https://codecov.io/gh/HelmholtzAI-Consultants-Munich/napari-organoid-counter/branch/main/graph/badge.svg)](https://codecov.io/gh/HelmholtzAI-Consultants-Munich/napari-organoid-counter)\n\n\nA napari plugin to automatically count lung organoids from microscopy imaging data. Note: this plugin only supports single-channel grayscale images.\n\n***Hold it for the demo!***\n\n![Demo](https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/blob/main/readme-content/demo-v026.gif?raw=true)\n\nThis demo showcases the features of Version 0.2.9.\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n\n## Installation\n\nThis plugin has been tested with python 3.11 - you may consider using conda or mamba to create your dedicated environment before running the `napari-organoid-counter`.\n\n1. You can install `napari-organoid-counter` via [pip](https://pypi.org/project/napari-organoid-counter/):\n\n    ``` pip install napari-organoid-counter```\n\n   To install for a developer:\n\n    ```git clone https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter```\n    ```pip install -e .```\n\nFor installing on a Windows machine directly from within napari, follow the instuctions [here](readme-content/How%20to%20install%20on%20a%20Windows%20machine.pdf).\n\n## Latest version features\nCheckout *Features of the latest version* [here](.napari/DESCRIPTION.md#whats-new-in-v3).\n\n## How to use?\n1. To launch the plugin directly from your terminal:\n```bash\nnapari -w napari-organoid-counter\n```\n\n2. For convenience you can add a shell alias  by adding this to your `~/.zshrc` (macOS) or `~/.bashrc` (Linux):\n```bash\nalias organoid='napari -w napari-organoid-counter'\n```\n\nThen reload your shell config:\n```bash\nsource ~/.zshrc   # macOS\nsource ~/.bashrc  # Linux\n```\n\nYou can now launch the plugin simply by running:\n```bash\norganoid\n```\n\n3. Alternatively, you can also start napari manually and select the plugin from the drop down menu.\n\nFor more information on this plugin, its intended audience, and a Quickstart guide go to our [Quickstart guide](.napari/DESCRIPTION.md#quickstart).\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [pytest], 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 ```BioIO```<sup>[1]</sup> for reading and processing images.\n\n[1] Eva Maxfield Brown, Dan Toloudis, Jamie Sherman, Madison Swain-Bowden, Talley Lambert, Sean Meharry, Brian Whitney, AICSImageIO Contributors (2023). BioIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub. https://github.com/bioio-devs/bioio\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[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, Francesco Campi, Abdulkader Ghandoura, & Piraud, M. (2026). HelmholtzAI-Consultants-Munich/napari-organoid-counter: v0.2.6 (v0.2.6). Zenodo. https://doi.org/10.5281/zenodo.19824587\n> \nbibtex:\n```\n@software{christina_bukas_2026_19824587,\n  author       = {Christina Bukas and\n                  Francesco Campi and\n                  Abdulkader Ghandoura and\n                  Piraud, Marie},\n  title        = {HelmholtzAI-Consultants-Munich/napari-organoid-\n                   counter: v0.2.6\n                  },\n  month        = apr,\n  year         = 2026,\n  publisher    = {Zenodo},\n  version      = {v0.2.6},\n  doi          = {10.5281/zenodo.19824587},\n  url          = {https://doi.org/10.5281/zenodo.19824587},\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":"Christina Bukas, Francesco Campi, Abdulkader Ghandoura","author_email":"francesco.campi@helmholtz-munich.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 :: 3.10","Operating System :: OS Independent","License :: OSI Approved :: MIT License"],"requires_dist":["numpy==1.26.4","napari[all]==0.7.0","bioio==3.3.0","bioio-ome-tiff==1.4.0","bioio-tifffile==1.3.0","bioio-imageio==1.3.0","bioio-czi==2.6.0","bioio-nd2==1.6.2","bioio-lif==1.4.0","bioio-dv==1.2.0","torch<=2.5.1","lxml_html_clean==0.4.4","torchvision==0.20.1","opencv-python==4.11.0.86","onnxruntime==1.23.0","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\""],"requires_python":">=3.11, <3.12","requires_external":null,"project_url":["Source Code, https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter","Documentation, https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter#README.md","Bug Tracker, https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/issues","User Support, https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}