ALIBY: End-to-end processing for high throughput microscopy

This framework orchestrates a multitude of different tools to process imaging data.

NOTE: This past year ALIBY went through heavy refactoring. The documentation is under (re)construction.

By modality:

• Time series microscopy
• Fluorescence microscopy (e.g., Cell Painting)

By procedure

• Segmentation (e.g., Cellpose) + Feature (e.g., cp_measure, engineered features)
• Deep Learning models (e.g., DinoV3, OpenPhenom)

By backend

• Within the same environment (Cellpose -> cp_measure)
• Communicating with other environments (via Nahual)

Installation

We recommend using uv to install aliby

Once uv is installed, we suggest running

git clone [email protected]:afermg/aliby.git
cd aliby
uv sync --all-extras

Nix installation

For reproducible environments using Nix flakes and envrc.

To run a self-contained virtual environment shell session

nix develop . 

For convenience, to start the environment every time you access the project you automatically set the environment

direnv allow .