End-to-end processing of cell microscopy time-lapses. ALIBY automates segmentation, tracking, lineage predictions and post-processing.
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 # --extra cellposeThis is still under works and it is not guaranteed to work as-is on MacOS, but in Linux running the Nix package manager it should make the setup trivial.
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 .