CirroCirrospatial data studio

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Look at and analyze spatial omics data in your browser

Open a Xenium, Visium or CosMx section and see every cell over the tissue image. Find clusters, compare groups and the genes that set them apart, and keep what you find as a version of the data, with nothing to install and no code to write.

Open the appRead the guide
Public DataPublic sections, ready to open, with no account. The analyses run in your browser, and nothing leaves it.Private Data (Cirro)Your own Cirro projects, read where they are stored, with each result saved back to the project for your team.
A Xenium pancreas section open in the web app: every cell drawn over the H&E image and colored by its cellular neighborhood, with the analysis tasks in a drawer on the left and the display settings in a drawer on the right.
A Xenium human pancreas section from Public Data, each cell colored by its cellular neighborhood over the H&E image. The analyses are in the drawer on the left and the display settings in the drawer on the right. Explore public data walks through it.

How it organizes your data

From the instrument to the figure

The web app sorts a project's data into four stages and shows them as a map. An item moves on to the next stage when a pipeline or an analysis makes it.

  1. Images

    Microscopy and histology images on their own, before any cells are found in them.

  2. Instrument runs

    An instrument's raw output as it wrote it: transcripts, its own cell segmentation, images and metrics.

  3. Spatial data

    Each cell with its position, expression and annotations, with the images and cell boundaries, and every version you save on it.

  4. Figures

    A view kept as a figure, saved inside the version it was made in.

Four stages of data has which Cirro datasets and files each stage reads, and what you can do at each.

Analyses with reports

Find clusters, compare groups, find marker genes and spatially variable genes, measure neighborhood enrichment and find cellular niches, all in your browser. Each opens as a report, and each follows scanpy and squidpy and is tested against them. Analyze in the browser.

Versions, not copies

What you make is saved as a version holding only what changed: a new column of labels is kilobytes, beside a store of gigabytes that is not copied. Nothing is ever overwritten, so going back is just opening an older version.

Work as a team

In Cirro, each version is a dataset in the project, with a note of what was saved and by whom. Anyone on the project can open it and save their own version on top. Your data in Cirro.

Figures you can publish

Keep the tissue as it is shown as a figure, or download it as SVG, PDF or a 300 dpi PNG, one or two columns or a slide wide.

Analysis Workspaces

When the browser isn't enough

An Analysis Workspace is the server version of Spatial Data Studio: every squidpy and scanpy function through point-and-click forms, curated recipes of several steps, and the memory of a whole machine for sections too big for a browser. The web app starts one in your Cirro project with the datasets you choose, attached in place, so nothing is downloaded and a section too big for a laptop only needs a bigger machine.

You pick a function, fill in a form built from that function's own signature, and it runs against the object in memory. The analysis adds its columns, embeddings and graphs to the object you already have, and appends one entry to the session's history. What the canvas can color by grows as you go.

Running a functionYour dataa run folder, or a.zarr the app savedspatialdata-ioreads it, live logyou pickCellular neighborhoodsn_neighborsn_clusterskey_addedthe form is the function's own signaturecitation·documentationevery function says where it came fromrunsThe object, in placeobs["neighborhood"]obsm["X_umap"]obsp["spatial"]history += one entryno undo, no copies:the log is the recorddrawsThe canvasevery cell, over the imagecolor by any column or genewhat you keep is chosen from what is thereSaving what you didWhat to keepimage · 2 levelscells · annotationsembeddingsexpression · 1.1 GBeach part priced,each one optionalwritesOne fileovary-neighborhoods.sdata.zarr.zipthe cells, the image pyramid, the shapes,the figures you drew, the display settings,and the history that produced all of itread by HTTP range requestsopensTwo ways back inin the app — history intact,and you can keep goingin a browser, from a URL,with no backend at allstreams what the view needsshareA link to a viewonly what you changedtravels, so it stays shorta colleague lands onyour view, not the saved one
One function, then the file it all ends up in. The top row is the loop you spend the day in; the bottom row is what leaves the machine. The checkpoint is one file rather than a folder because that is what a browser can read a few kilobytes out of — opening a 438 MB checkpoint and coloring by a gene costs under a megabyte. The checkpoint format has the layout; DESIGN.md has the reasoning.

An Analysis Workspace is one running app, and colleagues can join it once you share it. Whoever opens a session holds its edit lock; everyone else watches, and each analysis appears on their screens as it finishes rather than on a reload. What you are looking at stays yours — your gene, your channels, your corner of the section — while someone else drives.

Cirro project · one lab's dataeveryone signs in as themselvesDatasets · read onlyXenium · 412,000 cells · 34 GBVisium HD · 8 sectionsreferences · annotationsPublished resultsovary-neighborhoods · v3the checkpoints, and the viewer itself, so thedataset opens in a browser with nothing runningreads the datasetsnever writes thempublishes a checkpoint,only when you askanyone with accessto the projectSpatial Data Studio · one workspace in the projectpublic.ecr.aws/cirrobio/spatial-data-studio:v1Session · ovary-01edit lock: PriyaMarco is watchingSession · colon-04edit lock: Adaindependent of the otherthe workspace'sCPU and RAM,not yoursone URL, three browsersPriyaholds the lockruns the clusteringMarcosame sessionsees each step land;his own gene, his own zoomAdaher own sessiona different dataset,the same workspaceJunno app runningopens the publisheddataset in a browser
One project, one workspace, several people. The solid arrows are what the app does on its own, and they only read. The dashed ones are yours to take: publishing a finished checkpoint into the project, and someone else opening it. What each person's browser can see is what their own Cirro account can see — there is no shared account and no credential on the server.

Sign in as yourself

Sign-in is per browser, through Cirro's device-code flow: you open a link, sign in as you normally would, and the app never sees a password. The server holds no Cirro credential and needs no Cirro configuration, so several people share one running app without sharing an account.

Publishing is the one write

Saved checkpoints upload as a new dataset alongside the data rather than on top of it. The upload carries the viewer itself and an index of what is in it, so the resulting dataset opens as a browsable collection for anyone with access — no app, no install, no download.

Two people, one session

The padlock next to a session name says who holds it and who is on it, and names everyone in the room. Take an unlocked session, hand yours over, or rename yourself from the two-word name you arrived with. Watching costs nothing: display settings are per-browser and never enter the session.

An Analysis Workspace also runs on your own computer, from one Docker command: Run it with Docker, which also connects an AI assistant to it. Analysis Workspaces has starting one, sharing it and publishing from it; DESIGN.md §15 has the auth and credential scoping.

Advanced

The viewer on its own

A saved checkpoint opens in any browser with nothing running behind it. The viewer reads only what the current view needs, so opening a 438 MB checkpoint and coloring by a gene costs under a megabyte.

Copy a link to the exact view you are looking at, put a folder of checkpoints on any web server that answers range requests, or show the viewer in a frame on your own page or dashboard.

Share and embed the viewer · Live demos

<iframe src="viewer/index.html ?checkpoint=my-run.sdata.zarr.zip &embed=1"></iframe>