🔬 BIA Sanity Preserver 🧠

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.

🧩 The Idea

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.

🚀 Getting Started

All you need is:

1. pixi installed → pixi
2. This repository cloned:

git clone https://github.com/lorenzocerrone/BIA-Sanity-Preserver

That’s it. You’re officially on the path to BIA enlightenment.

🛠️ Tools Included

Run your tools with a single command and zero emotional damage:

• Cellpose
• Napari with OME-Zarr support
• ilastik
• Plant-seg
• Feature-explorer

🏗️ Environments

Ready-to-use environments for bio image analysis:

• Python Scientific Stack
• Ngio

🌠 Wish List

• StarDist
• ...

(Java-based tools are trickier to containerize with pixi, but it could be done!)

• Fiji / ImageJ2 (PoC available: pixi-fiji)

• QuPath

🤝 Contributing

Any contributions are welcome! Here’s how you can help:

• If something's not working, open an issue 🐛
• If you have ideas for new tools or improvements, open an issue 💡
• If you want to add a tool or improve an existing setup, submit a pull request 🚀

🧪 Testing

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.