spatialscapeOne fast map for every section.

A static, reactive browser for spatial transcriptomics and snRNA-seq. One pip install turns AnnData or SpatialExperiment into a dataset you can open locally or publish as a site.

Get started

Open the demo

GitHub

a human amygdala Visium section colored by spatial domain

🗺️

Every sample on one canvas

All sections of a study side by side under identical settings. Double-click to focus, step through donors with the arrow keys, switch platforms with one click.

⚡

Instant gene switching

Expression is stored one byte per cell per gene in sharded Zarr, so a gene is a single range request and a cached switch is a GPU upload.

🎨

Color, filter, gene sets

Color by gene, two blended gene sets, or any annotation. Filter independently of the colour, by a gene, a QC range or a category.

🔬

Hover, lasso, compare

Hover reads domain, cell type and expression. Lasso a region for composition, gene statistics and a CSV of cell IDs. A dot plot per annotation doubles as a filter.

🧬

Linked snRNA-seq

Paired references render as embeddings beside the tissue with one shared cell type vocabulary, so a color means the same thing everywhere.

📦

Static everywhere

No server. The app is files, the data is files. GitHub Pages, S3, Cloudflare R2, or a folder on a lab server with CORS and Range.

In three commands

bash

pip install spatialscape
spatialscape init analysis/spe_dlpfc.rds --id dlpfc      # writes dlpfc.yaml, a menu of what the data contains
spatialscape build dlpfc.yaml                            # -> bundles/dlpfc; rerun after any edit

Then open it, viewer included:

bash

spatialscape serve bundles --open

And when it is ready for others, spatialscape site build bundles -o site writes a folder to upload anywhere; a gallery of several datasets is described in a site.yaml. How it fits together shows which files you edit and which folders you upload.

Who it is for

Labs publishing spatial data. Put a dataset online alongside a paper without running a server, and give readers a link that opens the exact view you want them to see.

Analysts. Browse a million cells at 60 fps, check a marker across every donor at once, and lasso a region to see what is in it.

Institutes. A registry turns the viewer into a data portal, and an optional site bar lets it sit inside an institutional website.