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Attribute
Single-Cell & Spatial Biology

SpatialData

scverse Consortium
Choose a productChoose a product
CategorySingle-Cell & Spatial Biology
Companyscverse Consortium
PriceFree Open Source
StatusStatus not confirmed
AvailabilityAvailable on PyPI and GitHub
Last checked20/09/2026
FeaturesStandardized representation of spatial coordinates, images, labels, and feature tables, Support for 10x Visium, 10x Xenium, NanoString CosMx, Akoya PhenoCycler, and Vizgen MERSCOPE, Affine transformation engine for multi-modal spatial image co-registration, Zarr-based storage for fast streaming and out-of-memory computation
Entry typePython Library
Access modeOpen Source
AI roleSpatial Data Modeling & Alignment
Input dataNot recorded
Output dataNot recorded
Licence conditionsBSD-3-Clause
Commercial eligibilityPermissive open source release
Compute requirementsStandard Python environment (CPU/GPU)
ValidationNot recorded
TypeSpatial omics data standard and library
Intended useNot recorded
CompatibilityNot recorded
Manufacturerscverse Community
Biological applicationSpatial transcriptomics, multiplexed immunofluorescence, and tissue cartography
Research workflowLoad raw spatial instrument files -> align coordinates -> perform spatial statistics and Napari visualization
Evidence levelPeer-reviewed research (Nature Methods 2024)
Integration evidencehttps://spatialdata.scverse.org
Laboratory handoffEnables interactive histological exploration of spatial tissue biopsies