MNB Image Analysis Course Repo

This repo hosts materials and a website for the Image Analysis course offered by the Microscopy Network Basel (MNB).

The course introduces the fundamentals of (bio-)image analysis and focuses on Python-based workflows for its practical sessions.

Building the jupyter book locally

The website is built using Jupyter Book.

To build the jupyter book locally (e.g. to preview your changes to it), make sure you have jupyter-book installed. You can install it via pip:

pip install "jupyter-book<2"

Then, navigate to the root of this repository and run:

jupyter-book clean .
jupyter-book build . --all

The built book will be available in the _build/html folder. You can open the index.html file in your web browser to view it locally.

Notebook testing

The repo includes a GitHub Actions workflow to automatically verify that the Jupyter notebooks listed in testing/notebooks_to_test.txt run through in combination with the materials/environment.yml conda environment. This as well as the computer setup instructions can be replaced by pixi based workflows.