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3D simulated biological tissue sections with network-based spatial analysis and ABM-initialization workflows.
📚 Documentation site (canonical): https://emcramer.github.io/tissue_simulator/
The authoritative reference and tutorials — quickstart, guides, hand-written API guides, auto-generated per-symbol API reference, and the changelog. Versioned: a navbar switcher shows latest and each tagged release.
📊 Slide deck: a 13-slide visual tour of the package end-to-end (code + matplotlib output side by side) — tissue generation, slicing, spatial network analysis, replicate generation, cell-type assignment, reproducibility. Rendered from docs/slides/tour.ipynb on every release.
🛠️ Source: https://github.com/emcramer/tissue_simulator 🐛 Issues / feature requests: https://github.com/emcramer/tissue_simulator/issues
The docs site is authoritative reference and tutorials — versioned, generated from the package's source on each push to main and each tagged release. Edits go through pull requests.
The wiki (this site) is the low-friction community space — quick-answer FAQs, troubleshooting tips, and the rough-edged roadmap. Anyone with repo access can edit a page directly. When a wiki entry stabilizes and applies to all readers, promote it to the docs site.
- FAQ — frequently asked questions
- Troubleshooting — common errors and fixes
- Roadmap — what's planned, under consideration, and out of scope
- Getting started: Quickstart
- Visual tour: Slide deck
- Full workflow tutorial: Complete Workflow guide
- LLM integration: MCP guide
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API reference (per-symbol, auto-generated):
tissue·packing·graph_coloring·replicate_generator