Metadata-Version: 2.3
Name: organoid-analyzer
Version: 0.1.0
Summary: Analyze brightfield images of organoids
Author: Jian Wei Tay
Author-email: Jian Wei Tay <jian.tay@vai.org>
Requires-Dist: matplotlib>=3.11.0
Requires-Dist: numpy>=2.5.0
Requires-Dist: scikit-image>=0.26.0
Requires-Dist: scipy>=1.18.0
Requires-Dist: tqdm>=4.68.3
Requires-Python: >=3.14
Description-Content-Type: text/markdown

# Organoid analyzer

A Python tool for analyzing brightfield images of organoids.

## Usage

### Setup and installation

You can install the library directly either from PyPi or from this repository.

```bash
pip install organoid-analyzer
pip install "organoid-analyzer @ git+https://github.com/vaioic/organoid-analyzer.git@main"
```

If you need the latest bleeding-edge version (which likely contains bugs and other incomplete code)

```bash
pip install "organoid-analyzer @ git+https://github.com/vaioic/organoid-analyzer.git@dev"
```


## Development

### Using uv (Recommended)

This project uses [uv](https://docs.astral.sh/uv/) to manage the development environment.

1. Install ``uv``
    * **macOS or Linux:** ``curl -LsSf https://astral.sh/uv/install.sh | sh``
    * **Windows:** ``powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"``
    
    To check if you have ``uv`` installed, open a terminal and run ``uv --version``.

2. Clone the repository
   ```bash
   git clone git@github.com:vaioic/brightfield-organoid-analyzer.git
   cd brightfield-organoid-analyzer
   ```

3. Sync the environment (this will setup the correct virtual environment and dependencies)
   ```bash
   uv sync
   ```

3. Link this toolbox in editable mode in your analysis project
   ```bash
   uv add --editable "path/to/brightfield-organoid-analyzer"
   ```
   Note: You should change this to the published version when you are done.


### Code style and testing

This project also uses ``ruff`` for ultra-fast linting and code formatting, and ``pytest`` for unit tests.

```bash
# Run linting checks
uv run ruff check

# Auto-format codebase
uv run ruff format

# Run test suite
uv run pytest
```

## Issues

If you encounter any issues with running the code or have any questions, please create an [Issue](https://github.com/vaioic/brightfield-organoid-analyzer/issues) or send an email to opticalimaging@vai.org. If you are reporting a bug, please include any error messages to aid with troubleshooting.

## License

This project is licensed under the GPLv3 License. See the [LICENSE](LICENSE) file for details.

## Citing & Acknowledgements

This repository is publicly available for open-source use, but it is developed and maintained by the Optical Imaging Core at the Van Andel Institute. If code from this repository contributed to data used in a publication, abstract, or presentation, please cite and acknowledge our work based on your affiliation:

### For External Users
Please cite this repository and acknowledge the author(s) in your publication's materials, methods, or acknowledgements section:
> "Image analysis pipelines were adapted from open-source tools developed by the Optical Imaging Core at the Van Andel Institute (GitHub:[brightfield-organoid-analyzer](https://github.com/vaioic/brightfield-organoid-analyzer))."

If you require custom adjustments or advanced analysis support, please contact us at opticalimaging@vai.org.

### For Internal Users & Close Collaborators
If you are an internal researcher or an external collaborator working directly with our staff, please include our Research Resource Identifier (RRID) in your materials and methods section:
> "Image analysis and data processing were performed in collaboration with the Optical Imaging Core at the Van Andel Institute (RRID:SCR_021968)."

Please review the Acknowledgement and Authorship Guidelines on [VAI's Core Technology and Services website](https://vanandelinstitute.sharepoint.com/sites/Cores/SitePages/Acknowledgements-and-Authorship.aspx)

### Contributors
<a href="https://github.com/vaioic/brightfield-organoid-analyzer/graphs/contributors">
  <img src="https://contrib.rocks/image?repo=vaioic/brightfield-organoid-analyzer" />
</a>

## Changelog

### v0.1.0 (2026-07-03)
* Adapted code into a toolbox.
* Test that code works on EB cells [[OIC-334](https://varioic.atlassian.net/browse/OIC-334)]