articleNature MethodsMar 20, 2024HYBRID OA

SpatialData: an open and universal data framework for spatial omics

LMLuca MarconatoGPGiovanni PallaKAKevin A. YamauchiIVIsaac VirshupEHElyas Heidari

German Cancer Research Center · Heidelberg University · +10 more institutions

PubMed
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Abstract

Spatially resolved omics technologies are transforming our understanding of biological tissues. However, the handling of uni- and multimodal spatial omics datasets remains a challenge owing to large data volumes, heterogeneity of data types and the lack of flexible, spatially aware data structures. Here we introduce SpatialData, a framework that establishes a unified and extensible multiplatform file-format, lazy representation of larger-than-memory data, transformations and alignment to common coordinate systems. SpatialData facilitates spatial annotations and cross-modal aggregation and analysis, the utility of which is illustrated in the context of multiple vignettes, including integrative analysis on a…

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169
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Authors

22

Topics & keywords

Topics
Keywords
  • Computer science
  • Context (archaeology)
  • Representation (politics)
  • Omics
  • Spatial analysis
  • External Data Representation
  • Data science
  • Data mining
UN Sustainable Development Goals
  • Good health and well-being
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