Words this guide uses
Spatial Data Studio uses a few words in a particular sense. Each is defined here, with a link to where the guide covers it.
Analysis Workspace
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. It runs as a workspace in your Cirro project, started from the web app, or on your own computer with Docker. Analysis Workspaces.
Annotation
A column of a store's table with one value per cell: a grouping, such as clusters, cell types or the areas you labelled, or a number, such as a quality metric. You color the cells by an annotation, and an analysis that works on groups takes a grouping of 2 to 100 groups. In SpatialData it is a column of the table's obs.
Cell, spot
What each point on the tissue is. Most platforms measure cells; Visium measures capture spots, and the app says spots rather than cells for a Visium store.
Checkpoint
A store Spatial Data Studio saved whole, as one .sdata.zarr.zip file: what an Analysis Workspace saves, and what Spatial Data Studio's workflow makes of an instrument run. It carries copies made for fast reading, so it opens quickly in the web app, in an Analysis Workspace, or in the viewer on its own. A version is different: it holds only what changed.
Cirro
The data platform Spatial Data Studio is built with. Your organization has its own Cirro, at its own address, and you log in to it to open your projects. Your Data (Cirro).
Dataset
Cirro's unit of data in a project: an upload, a pipeline's output, or a version the app saved. One dataset can hold several items (several stores, runs or images), and the map shows each one. The guide also says dataset for the item you open.
Expression matrix
Each cell's count of each gene: the table's X. Coloring by a gene and the gene analyses read it. A store saved without it still offers labelling, neighborhoods, niches and figures.
Figure
A view kept with its colors and framing (the tissue or the cell map), or a chart from a report. A figure is kept inside the version it was made in, or downloaded as SVG, PDF or a 300 dpi PNG. Figures are the fourth stage. Keep a figure.
Instrument run
An instrument's raw output as it wrote it (Xenium, Visium, CosMx, MERSCOPE and others): the transcripts or spots, the instrument's own cell segmentation, the images and the run's metrics. It isn't SpatialData yet: a pipeline makes a store of it. Instrument runs are the second stage.
Map
What a project opens as: its items as bubbles in four columns, one per stage, with dashed lines joining a run or an image to the spatial data made from it. The map.
Project
Where data lives. A Cirro project holds a team's datasets, and your role in it decides what you can do there; a public project is one anyone can open with no account. Every project is either one you can add to or a read-only one. Projects.
Public Data
The public projects the web app opens on, starting with Spatial Data Studio's own examples, which anyone can open with no account. Settings adds others, including your own. Public Data.
Read-only
A project you can look at and analyze but not add to: every public project, and a Cirro project where your role lets you only view. What you save there is kept in this browser, where nobody else can see it.
Report
What an analysis opens as when it finishes: what was run and with which settings, the numbers that sum it up, its charts, a card for each group and the full table. It is kept with the data. Reports.
Section
A tissue section: the thin slice of tissue an instrument measured, and what you look at in the app. A store holds a section's cells, images and cell boundaries. Look at a section.
Session
In an Analysis Workspace, one dataset opened to work on, held in the workspace's memory. Whoever opens it holds its edit lock, and others can watch. Work in it together.
SpatialData
The open format (spatialdata.scverse.org) that analysis-ready spatial data is kept in: a section's cells, with their positions, expression and annotations, together with its images and cell boundaries. Spatial data, the third stage, is data in this format.
Stage
One of the four kinds of data the web app works with, in order: Images, Instrument runs, Spatial data and Figures. An item moves on to the next stage when a pipeline or an analysis makes it. Four stages of data.
Store
One SpatialData store: a .zarr.zip file or a .zarr folder holding a section's cells, images and cell boundaries. Opening a store is what shows a section. A checkpoint is a store Spatial Data Studio saved whole; a version is read over the store it was saved on.
Unsaved changes
What tasks have made since you last saved, shown in a bar at the bottom of the page. They are kept in this browser, so a reload loses nothing, until you save them as a version or discard them. Save a version.
Version
What the web app saves: only what changed (a new column of labels, a report, a figure), on top of the store or version it was saved on, so a column of labels is kilobytes beside a store of gigabytes. In a project you can add to, each version is a new dataset; in a read-only one, it is kept in this browser. Nothing is overwritten, so going back is opening an older version. Versions and history.
Viewer
The part of Spatial Data Studio that draws a section. On its own, it opens a checkpoint in any browser with nothing running behind it, and it can sit in a frame on another page. Share and embed the viewer.
Web app
Spatial Data Studio in your browser, at spatial-studio.apps.cirro.bio, with nothing to install. It opens Public Data and your Cirro projects, and its analyses run in your browser. Introduction.
Workflow
Spatial Data Studio's Nextflow pipeline. It reads an instrument run with its platform's reader, runs the standard analysis for that kind of data, and saves the result as a checkpoint. nextflow/README.md.