organoid-analyzer 0.1.0

Analyze brightfield images of organoids

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.

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)

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

Development

Using uv (Recommended)

This project uses 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

   git clone [e-mail]:vaioic/brightfield-organoid-analyzer.git
   cd brightfield-organoid-analyzer
   

3. Sync the environment (this will setup the correct virtual environment and dependencies)

   uv sync
   

4. Link this toolbox in editable mode in your analysis project

   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.

# 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 or send an email to [e-mail]. 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 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)."

If you require custom adjustments or advanced analysis support, please contact us at [e-mail].

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

Contributors

Changelog

v0.1.0 (2026-07-03)

• Adapted code into a toolbox.
• Test that code works on EB cells [OIC-334]