Process and analyse live-cell and/or fluorescence imaging data
Project description
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 git@github.com: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 .
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