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 installing both ALIBY and WELA.

To begin you should install miniconda and poetry.

Once poetry is installed, we suggest running

poetry config virtualenvs.create false

so that only conda creates virtual environments.

Then

• Create and activate an alibylite virtual environment

conda create -n alibylite python=3.10
conda activate alibylite

• Git clone alibylite, change to the alibylite directory with the poetry.lock file, and use poetry to install:

poetry install

• Git clone wela, change to the wela directory with the poetry.lock file, and use poetry to install:

poetry install

• Use pip to install your usual Python working environment. For example:

pip install ipython seaborn

• Install omero-py.

For a Mac, use:

conda install -c conda-forge zeroc-ice==3.6.5
conda install omero-py

For everything else, use:

poetry install --all-extras

• You may have an issue with Matplotlib crashing. Use conda to install a different version:

conda search -f matplotlib       

and, for example,

conda install matplotlib=3.8.0 

• On an M1 Mac, these commands proved helpful

conda install openblas
conda uninstall numpy
conda install numpy    

and reinstalling tensorflow

python -m pip install tensorflow-macos==2.9.0 tensorflow-metal==0.5.0 --force-reinstall

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 flakes and envrc.

To run a self-contained virtual environment shell session

nix develop . --impure

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

direnv allow . 

IDE Integration

Doom Emacs

Activate the direnv module (under :tools) on Doom's init.el. Then add this to your config.el.

(require 'envrc)
(add-hook! (add-hook 'change-major-mode-after-body-hook 'envrc-mode))

That should ensure that Emacs finds the activated environment when running (run-python) from a Python file inside the environment.