Metadata-Version: 2.4
Name: napari-organoid-counter
Version: 0.2.9rc1
Summary: A plugin to automatically count lung organoids using Deep Learning.
Home-page: https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter
Author: Christina Bukas, Francesco Campi, Abdulkader Ghandoura
Author-email: francesco.campi@helmholtz-munich.de
License: MIT
Project-URL: Source Code, https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter
Project-URL: Documentation, https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter#README.md
Project-URL: Bug Tracker, https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/issues
Project-URL: User Support, https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/issues
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 :: 3.10
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.11, <3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy==1.26.4
Requires-Dist: napari[all]==0.7.0
Requires-Dist: bioio==3.3.0
Requires-Dist: bioio-ome-tiff==1.4.0
Requires-Dist: bioio-tifffile==1.3.0
Requires-Dist: bioio-imageio==1.3.0
Requires-Dist: bioio-czi==2.6.0
Requires-Dist: bioio-nd2==1.6.2
Requires-Dist: bioio-lif==1.4.0
Requires-Dist: bioio-dv==1.2.0
Requires-Dist: torch<=2.5.1
Requires-Dist: lxml_html_clean==0.4.4
Requires-Dist: torchvision==0.20.1
Requires-Dist: opencv-python==4.11.0.86
Requires-Dist: onnxruntime==1.23.0
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: napari; extra == "testing"
Requires-Dist: pyqt5; extra == "testing"
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: license
Dynamic: license-file
Dynamic: project-url
Dynamic: provides-extra
Dynamic: requires-dist
Dynamic: requires-python
Dynamic: summary

# Napari Organoid Counter - Version 0.2.9 is out! 

[![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)
![stability-stable](https://img.shields.io/badge/stability-stable-green.svg)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6457903.svg)](https://doi.org/10.5281/zenodo.6457903)
[![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)
[![PyPI](https://img.shields.io/pypi/v/napari-organoid-counter.svg?color=green)](https://pypi.org/project/napari-organoid-counter)
[![Python Version](https://img.shields.io/badge/python-3.11-blue)](https://python.org)
[![tests](https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/workflows/tests/badge.svg)](https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/actions)
[![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)


A napari plugin to automatically count lung organoids from microscopy imaging data. Note: this plugin only supports single-channel grayscale images.

***Hold it for the demo!***

![Demo](https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter/blob/main/readme-content/demo-v026.gif?raw=true)

This demo showcases the features of Version 0.2.9.

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

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


## Installation

This 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`.

1. You can install `napari-organoid-counter` via [pip](https://pypi.org/project/napari-organoid-counter/):

    ``` pip install napari-organoid-counter```

   To install for a developer:

    ```git clone https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter```
    ```pip install -e .```

For installing on a Windows machine directly from within napari, follow the instuctions [here](readme-content/How%20to%20install%20on%20a%20Windows%20machine.pdf).

## Latest version features
Checkout *Features of the latest version* [here](.napari/DESCRIPTION.md#whats-new-in-v3).

## How to use?
1. To launch the plugin directly from your terminal:
```bash
napari -w napari-organoid-counter
```

2. For convenience you can add a shell alias  by adding this to your `~/.zshrc` (macOS) or `~/.bashrc` (Linux):
```bash
alias organoid='napari -w napari-organoid-counter'
```

Then reload your shell config:
```bash
source ~/.zshrc   # macOS
source ~/.bashrc  # Linux
```

You can now launch the plugin simply by running:
```bash
organoid
```

3. Alternatively, you can also start napari manually and select the plugin from the drop down menu.

For more information on this plugin, its intended audience, and a Quickstart guide go to our [Quickstart guide](.napari/DESCRIPTION.md#quickstart).

## Contributing

Contributions are very welcome. Tests can be run with [pytest], 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-organoid-counter" is free and open source software

## Dependencies


```napari-organoid-counter``` uses the ```BioIO```<sup>[1]</sup> for reading and processing images.

[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

## 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/HelmholtzAI-Consultants-Munich/napari-organoid-counter/issues

[napari]: https://github.com/napari/napari
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/

## Citing

If you use this plugin for your work, please cite it using the following:

> 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
> 
bibtex:
```
@software{christina_bukas_2026_19824587,
  author       = {Christina Bukas and
                  Francesco Campi and
                  Abdulkader Ghandoura and
                  Piraud, Marie},
  title        = {HelmholtzAI-Consultants-Munich/napari-organoid-
                   counter: v0.2.6
                  },
  month        = apr,
  year         = 2026,
  publisher    = {Zenodo},
  version      = {v0.2.6},
  doi          = {10.5281/zenodo.19824587},
  url          = {https://doi.org/10.5281/zenodo.19824587},
}
```
