Because setting up bio image analysis tools shouldn’t cost you your sanity.
Setting up bio image analysis (BIA) tools the sane way is hard. Requirements change. Dependencies fight. Conflicts arise. Environments grow tangled and break.
BIA Sanity Preserver is here to restore balance.
With it, you can install and run your favourite bio image analysis tools in clean, isolated environments, avoiding conflicts and keeping your workflows reproducible and drama-free.
In one work, use pixi. No containers, no complexity, just pure, isolated environments.
📦 Each tool gets its own dedicated environment. ⚡ Environments can be quickly created, fearlessly modified (thanks to pixi locks 🔒), and easily deleted.
All you need is:
- pixi installed → pixi
- This repository cloned:
git clone https://github.com/lorenzocerrone/BIA-Sanity-PreserverThat’s it. You’re officially on the path to BIA enlightenment.
Run your tools with a single command and zero emotional damage:
Ready-to-use environments for bio image analysis:
- StarDist
- ...
(Java-based tools are trickier to containerize with pixi, but it could be done!)
-
Fiji / ImageJ2 (PoC available: pixi-fiji)
-
QuPath
Such a project can only thrive with the help of the community, to make sure that it stays up-to-date and useful for everyone. Here’s how you can contribute:
- If you have ideas for new tools or improvements, open an issue 💡
- If you test some tools, and had an issue let us know by opening an issue 🐛
- If you know your way around pixi and want to add a tool or improve an existing setup, submit a pull request 🚀
- If the documentation is lacking or unclear, feel free to suggest improvements via pull requests ✍️
Each environment is automatically installed on Ubuntu, macOS, and Windows using GitHub Actions to ensure cross-platform compatibility. The tools themselves are not tested beyond installation.