Notebooks / Tutorials (Very Detailed, Step-by-Step)#
These are long-form, notebook-style tutorials for the Cellucid Python package. They are intentionally thorough:
every step is explained,
edge cases and “gotchas” are called out,
and each tutorial ends with a large troubleshooting section.
Note
These pages are written in MyST and live in docs/user_guide/python_package/f_notebooks_tutorials/.
The runnable .ipynb entries use the real Pancreas H5AD checked into this
repository. The docs site does not execute notebooks during the build
(nb_execution_mode = "off"), so run them locally to interact with the
embedded viewer.
How to use this section, expected prerequisites, and how to run the notebooks reliably.
“I have an AnnData and I just want to see my cells.” Minimal choices, maximum clarity.
Reproducible exports, scaling workflows, and practical “do this when…” guidance.
Hooks, session mechanics, vector fields, and format-level debugging.
A complete, executable Pancreas preparation workflow you can adapt to your data.
A real Pancreas notebook for embedding, Python↔frontend events, and session bridging.