Skip to content

Roadmap

Jump to bottom
Eric Cramer edited this page May 28, 2026 · 1 revision

Roadmap

tissue_simulator is a research tool for generating spatially-similar replicates of biological tissue sections. Releases follow Semantic Versioning; the CHANGELOG is the canonical history.

This page captures forward-looking work that hasn't landed yet. Anything here is a candidate, not a commitment — comment on the linked issue (or open a new one) if you want it prioritized.

Under consideration

  • Multi-scale objective term in ReplicateGenerator. A meso-scale matching term (radial density profile, cross-type Ripley's L(r) at a few radii) on top of the current contact-statistics objective, so replicates of strongly structured sources (tumor disc / fibroblast ring / CD8 annulus) preserve morphology rather than flattening to a uniform mix. Flagged in the v0.1.7 spec sheet as a possible future request.
  • ReplicateGenerator composing GraphColorizer internally. Today they're separate stages glued together by TissueWorkflow. Folding annealing-based label assignment into ReplicateGenerator would make a single generate_replicates call work on structured multi-type targets without the two-stage workflow. The v0.1.9 docs answer this as a documentation question for now; a code change would be a v0.2.x candidate.
  • Executable notebook gallery on the docs site. mkdocs-jupyter would let the Quickstart / Complete Workflow render as runnable notebooks with output. Adds CI cost; probably worth it for a paper artifact.
  • PhysiCell round-trip tests in CI. v0.1.1 added the bridge and v0.1.6 documented it, but the round-trip from TissueSection → PhysiCell CSV → reloaded TargetStatistics → matching replicate is currently exercised by example scripts, not unit tests.
  • A test-running / lint GitHub Actions workflow. The docs site CI is the only workflow in the repo today (.github/workflows/docs.yml). A tests.yml running pytest on push and PR is the obvious next addition.
  • Custom domain for the docs site. Currently at emcramer.github.io/tissue_simulator/; switching to a project-specific domain is a trivial CNAME addition.

Out of scope (intentionally)

  • A built-in optimization for structured/regional placement (concentric rings, discs, annuli). External tooling (e.g. PhysiCell) handles structured layouts; the package then ingests them via the v0.1.7 / v0.1.8 coordinate-CSV API.
  • A general agent-based simulation loop. tissue_simulator is an initial-condition generator, not an ABM.

Releases at a glance

  • v0.1.10 (2026-05-28) — first deployed docs site, mike versioning, GitHub Actions docs workflow, wiki seed.
  • v0.1.9 (2026-05-28) — seedable GraphColorizer, assign_cell_types MCP tool.
  • v0.1.8 (2026-05-27) — MCP tools for coordinate-CSV ingest.
  • v0.1.7 (2026-05-26) — TissueSection.from_cells, load_tissue_from_csv, load_target_statistics_from_coordinates.

See the full CHANGELOG for prior versions.

Want to influence prioritization?

Open or upvote a GitHub issue: https://github.com/emcramer/tissue_simulator/issues. PRs welcome — the Contributing guidance is on the docs site (link to come once a contribution guide lands).

Clone this wiki locally