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Tour

A code-driven, end-to-end tour of tissue_simulator — every section shows the Python that produced it alongside the rendered matplotlib output, so you can see the package's surface area at a glance. Useful for talks, papers, and onboarding new users.

The tour is generated by executing a single Marimo notebook (docs/slides/tour.py) in CI on every push to main and every release tag, so what you see here is always in sync with the code.

Open the tour →

On the tour

  • Create a 3D tissue with TissueSection + sphere packing
  • Multi-type tissues (cancer / immune / stroma)
  • 2D slicing (TissueSlicer)
  • Slice in 3D context (slice plane + tissue overlay)
  • Spatial network construction (SpatialNetworkAnalyzer)
  • Per-type interaction statistics
  • Replicate generation (ReplicateGenerator)
  • Cell-type assignment via simulated annealing (GraphColorizer)
  • Reproducibility from a seed=

Run it yourself

pip install -e ".[docs]"
python docs/slides/build_tour.py
open docs/slides/tour.html

Source notebook (tour.py)