Notebooks

We encourage you to follow along with your own, fresh notebook, using the executed and rendered notebooks included in this repository only as a guide.

Rendered notebooks

• Bioimage visualization in Python
• Interactive analysis with Jupyter notebook, napari, scikit-image, and scipy
• Segmenting nuclei with the stardist napari plugin
• Bonus: Quantify nuclei shape
• Manual annotation
• Using custom colormaps in napari
• Conclusions
• Alternative notebooks

Note

In this repository, all notebooks have been converted to MyST Markdown files (with a .md extension) since this format is easier to visualize on GitHub. This also makes it easier to view differences between versions of the notebooks on the GitHub interface. To open these files as Jupyter Notebooks, you need to have the Jupytext package installed, see the notebook setup page..)

In the Jupyter notebook interface, if you right-click any of the .md files in this folder now, you should see an option that says “Open with -> Notebook”

Alternatively, you can also convert the .md files into .ipynb files by running

jupytext --to ipynb <notebook_file>.md

in the command line.