Spatial Data Studio

Interactive analysis and visualization for spatial omics data — in the browser, no code required.

Open a spatial transcriptomics dataset (Xenium, Visium, Visium HD, CosMx, MERSCOPE, or anything else SpatialData can read), run squidpy and scanpy analyses on it through point-and-click forms, and explore the result on a fast WebGL canvas that draws every cell over the tissue image. It runs as a single local server you open in your browser.

A whole Xenium ovarian-cancer section (~400,000 cells), colored by cellular neighborhood.

Run it

Everything ships as one Docker image, so the published build needs nothing but Docker and a folder of your own data:

docker run -d -p 8080:8888 \
  -v "$(pwd)/data":/data -e SDS_DATA_DIR=/data \
  public.ecr.aws/cirrobio/spatial-data-studio:v1

Open http://localhost:8080 and start a session on anything in that folder. docker/README.md has the compose file, the memory limits and the full environment contract; DEVELOPMENT.md has how to run from a clone instead. Or try it with nothing installed at all — the live demos are the real viewer running in your browser.

Documentation

cirrobio.github.io/spatial-data-studio renders every file below, so the same words read the same on GitHub and on the site.

User guide	what the app does — the source of truth for it
Run with Docker	the image, its memory limits and environment
Analysis methods	what each bundled method does
Development guide	architecture, repo layout, dev setup, tests
Design	the full specification and the reasoning behind it
API contract	the REST / SSE / Arrow contract
Contributing	adding a recipe or an analysis function
License	the Cirro Bio Source Available License

The default licence grant covers evaluation, review, and preparing contributions; any other use, including production use, needs a written authorization from Cirro Bio, Inc.

Maintenance rule: this README stays a short orientation — the pitch, how to run the app, and where the docs are. docs/USER_GUIDE.md is the source of truth for what the app does, and DEVELOPMENT.md for the developer-facing detail. Any change that adds, removes, or alters a user-facing capability updates the user guide in the same commit (and refreshes a screenshot if it materially changes a pictured panel); a change to the run command updates this README. See CLAUDE.md.