Metadata-Version: 2.4
Name: aliby
Version: 0.2.1
Summary: Process and analyse live-cell and/or fluorescence imaging data
Author-email: Alan Munoz <alan@quasimorphic.com>, Peter Swain <peter.swain@ed.ac.uk>
License-File: LICENSE
Requires-Python: <3.13,>=3.10
Requires-Dist: cellpose>=3.1.1.1
Requires-Dist: centrosome>=1.3.2
Requires-Dist: cp-measure<0.2,>=0.1.7
Requires-Dist: dask>=2021.12.0
Requires-Dist: loguru>=0.7.3
Requires-Dist: nahual>=0.0.6
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

# 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](https://github.com/MouseLand/cellpose)) + Feature (e.g., [cp_measure](https://github.com/afermg/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](https://github.com/afermg/nahual))

## 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 --all-extras
```

## Nix installation
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 . 
```

