Spatial Data Studio

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

Documentation → cirrobio.github.io/spatial-data-studio

User guide — everything the app does · Live demos — the real viewer, nothing to install · Run with Docker · Development guide

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

The quickest way to try it on your own machine is the single Docker image:

python scripts/prepare_test_data.py     # writes test-data/visium_hne.zarr (~375 MB, needs squidpy)
docker compose up --build -d            # builds the SPA + backend into one image
open http://localhost:8080              # New Session -> /data/visium_hne.zarr

The compose file bind-mounts a single read-write data directory at /data, holding inputs, saved checkpoints, and snapshots together. It defaults to test-data/; point it at your own folder with SDS_DATA_HOST_DIR (env var or .env entry), e.g. SDS_DATA_HOST_DIR=/path/to/data docker compose up. Memory limits, the manual docker run form, and the full environment contract are in docker/README.md. To run from source for development instead, see DEVELOPMENT.md.

All the documentation

The site above is rendered from these files, so they read the same on GitHub.

For users:

• docs/USER_GUIDE.md — what the app does: loading data, running analyses and recipes, the canvas and display settings, annotating and subsetting, sharing sessions, saving checkpoints and snapshots, the AI assistant, the no-backend checkpoint viewer, and uploading to Cirro.
• docker/README.md — running the Docker image, its memory limits and environment contract.
• backend/app/registry/custom/README.md — what each bundled analysis method does.

For developers:

• DEVELOPMENT.md — architecture, repo layout, where to make a change, local dev setup, tests, and the offline CLI.
• DESIGN.md — the full design specification and the reasoning behind it.
• docs/CONTRACT.md — the REST / SSE / Arrow API contract.
• CONTRIBUTING.md — add a recipe (one JSON file) or a custom analysis function, and the Contributor Policy those contributions are accepted under.
• LICENSE.md — the Cirro Bio Source Available License. The default 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.