scikit-image tutorial at EuroSciPy 2024

This repository contains the teaching materials for the scikit-image tutorial at EuroSciPy 2024.

Important

The tutorial is intended to be run in the browser.
Open the online tutorial here!

Contributing

Run notebooks in local environment

Updating the notebooks is best accomplished inside a local environment. Create a new virtual environment with Python 3.12 and install the dependencies into it with

python -m pip install -r requirements/local_dev.txt

If you want to add a dependency to local_dev.txt, add it to the corresponding local_dev.in instead and run

uv pip compile -o requirements/local_dev.txt requirements/local_dev.in

Build & serve website locally

Setup the required dependencies with

python -m pip install -r requirements/jupyterlite.txt

This repository stores the notebooks in markdown format with the help of Jupytext which is not yet supported by JupyterLite. So we need to convert the notebooks into the ipynb format with

find tutorial/ -name "*.md" -exec jupytext --to ipynb {} \;

then build & serve the site:

jupyter lite build --contents tutorial/
jupyter lite serve

If you want to add a dependency to jupyterlite.txt, add it to the corresponding jupyterlite.in instead and run

uv pip compile -o requirements/jupyterlite.txt requirements/jupyterlite.in

Acknowledgements

Builds on the original scikit-image tutorials, last years tutorial at EuroSciPy 2023 by Guillaume Lemaitre, and the joined image analysis tutorial at SciPy 2024.