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