Preparation of the session

To prepare this session, create a new python environment as explained below. It may furthermore be handy to download the contents of the repository for the exercises:

git clone https://github.com/scaDS/embl-bia-2026
cd embl-bia-2026

Alternatively, download the github repository as zip file, unzip it and navigate to its folder using the terminal. For example, if you unpacked it on your desktop:

cd Desktop/embl-bia-2026

uv

If you prefer using uv, you can setup the environment like this (from within the root folder rag-2026):

uv sync

You can then explore the notebooks using:

uv run jupyter lab

Conda

If you prefer using conda, it is recommended to setup a new environmment with Python 3.12 like this:

conda create --name bia26 python=3.12

You can then activate this environment like this:

conda activate bia26

And install all requirements

pip install openai jupyterlab pandas stackview numpy scikit-image python-dotenv bia-bob cellpose pyclesperanto

You can then explore the notebooks using:

jupyter lab