Metadata-Version: 2.4
Name: aliby
Version: 0.2.0
Summary: Process and analyse live-cell imaging data
Author-email: Alan Munoz <alan@quasimorphic.com>, Peter Swain <peter.swain@ed.ac.uk>
License-File: LICENSE
Requires-Python: <3.12,>=3.9
Requires-Dist: centrosome>=1.3.1
Requires-Dist: cp-measure<0.2,>=0.1.7
Requires-Dist: dask>=2021.12.0
Requires-Dist: loguru>=0.7.3
Requires-Dist: numpy>=1.18
Requires-Dist: pandas>=2.3.2
Requires-Dist: pooch<2,>=1.8.2
Requires-Dist: pyarrow>=19.0.1
Requires-Dist: scikit-image>=0.18.1
Requires-Dist: scikit-learn>=1.2.2
Requires-Dist: scipy>=1.7.3
Requires-Dist: zarr>=2.14.0
Provides-Extra: cellpose
Requires-Dist: cellpose>=3.1.1.1; extra == 'cellpose'
Description-Content-Type: text/markdown

# ALIBYlite (Analyser of Live-cell Imaging for Budding Yeast)

End-to-end processing of cell microscopy time-lapses. ALIBY automates segmentation, tracking, lineage predictions and post-processing.

## Installation

We recommend using [uv](https://github.com/astral-sh/uv) to install aliby

Once uv is installed, we suggest running

```bash
git clone git@github.com:afermg/aliby.git
cd aliby
uv sync # --extra cellpose
```

## Nix installation (experimental)
This 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](https://github.com/NixOS/nix) flakes and [envrc](https://github.com/numtide/devshell).

To run a self-contained virtual environment shell session
```bash
nix develop . 
```
For convenience, to start the environment every time you access the project you automatically set the environment
```bash
direnv allow . 
```

