Beta Release of Spatial Data on Census!

Published: Jan 14, 2025
By: Cathy Stolitzka, Isaac Virshup, Maximilian Lombardo

The Census team is pleased to announce the release of Spatial data on Census!

This has been a large joint effort between the Census team and TileDB to create an easy-to-use and backwards-compatible spatial schema that enables easy analysis with non-spatial and spatial data!

This first release is a beta release with the ability to export all spatial data (10x Visium Spatial Gene Expression and Slide-seqV2) from an obs/var query to SpatialData (spatialdata.scverse.org). The ability to query census with spatial-based filters, transforms, etc., is not supported and will be implemented in a future release.

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SOMA Spatial Data Model

Building Blocks

tiledbsoma.Experiment

A collection encapsulating data from one or more single-cell datasets, with reserved attributes:

Field Name	Field Description
obs	A DataFrame for observation metadata
ms	A collection (Measurement), with cell-by-gene data matrices and a gene metadata DataFrame
[NEW] spatial	A collection of Scene objects (see below)
[NEW] obs_spatial_presence	A DataFrame to map observations to Scene objects

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[NEW] tiledbsoma.Scene

A collection of spatial assets. All assets in one Scene should correspond to the same physical coordinate system. The collection provides operations for getting, setting, and transforming between coordinate systems, with reserved attributes:

Field Name	Field Description
obsl	A collection of spatial arrays and collections. The rows in these arrays correspond to observations and may correspond to obs of an Experiment.
varl	A collection of collections for spatial arrays on the Measurements. The top-level collection is indexed by measurement name. The rows in the contained arrays correspond to features and may correspond to var of the associated Measurement.
img	A Collection of MultiscaleImages

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[NEW] tiledbsoma.MultiscaleImage

A group of multi-resolution images that can be accessed by levels. Below are some sample operations on this collection type. Every DenseNDArray in the collection must be mappable to the same physical space by scaling only.

Operation	Description
.levels()	Returns a mapping of {member_name: (uri, shape)}.
coordinate_space	Coordinate space for the base level of this MultiscaleImage
get_transform_to_level / get_transform_from_level	Get ScaleTransform to and from specified level to base level of image