Python for BioImage Analysis

For students

For instructors

Set up

During development python scripts and notebooks in solutions/ are kept in sync using jupytext. You should install the jupytext VSCode extension to maintain both ways synchronization between notebooks and scripts

• Install the jupytext VSCode extension.
• Install pre-commit

  uv run pre-commit install

• Modify the python scripts in solutions/.
• To create the notebook from the script you can run:

  uv run jupytext solutions/05_image_analysis_with_skimage.py --sync

• Keep it out of git tracking, and let the VSCode extension sync the modification from ipynb to py

Implementing the modules

Exercises should be marked with the following clause:

# --- Exercise
<code>
# ---

Markdown cells are written in the following format:

# %% [markdown]
# <some markdown>
#

Code cells as:

# %%

Pushing new content

Please open a PR for new content, fixes, refactoring etc.