SpatialData: an Open and Universal Data Framework for Spatial Omics

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2024 Mar 21

PMID 38509327

Authors

Luca Marconato

Giovanni Palla

Kevin A Yamauchi

Isaac Virshup

Elyas Heidari

Tim Treis

Wouter-Michiel Vierdag

Marcella Toth

Sonja Stockhaus

Rahul B Shrestha

Benjamin Rombaut

Lotte Pollaris

Laurens Lehner

Harald Vohringer

Ilia Kats

Yvan Saeys

Sinem K Saka

Wolfgang Huber

Moritz Gerstung

Josh Moore

Fabian J Theis

Oliver Stegle

Affiliations

Soon will be listed here.

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 multimodal Xenium and Visium breast cancer study.

Citing Articles

Application of Spatial Omics in the Cardiovascular System.

Hu Y, Jia H, Cui H, Song J Research (Wash D C). 2025; 8:0628.

PMID: 40062231 PMC: 11889335. DOI: 10.34133/research.0628.

Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment.

Moses L, Huseynov A, Rich J, Pachter L bioRxiv. 2025; .

PMID: 40060564 PMC: 11888365. DOI: 10.1101/2025.02.24.640007.

Towards the Next Generation of Data-Driven Therapeutics Using Spatially Resolved Single-Cell Technologies and Generative AI.

Rodov A, Baniadam H, Zeiser R, Amit I, Yosef N, Wertheimer T Eur J Immunol. 2025; 55(2):e202451234.

PMID: 39964048 PMC: 11834372. DOI: 10.1002/eji.202451234.

Integrative co-registration of elemental imaging and histopathology for enhanced spatial multimodal analysis of tissue sections through TRACE.

Lu Y, Han S, Srivastava A, Shaik N, Chan M, Diallo A Bioinform Adv. 2025; 5(1):vbaf001.

PMID: 39829713 PMC: 11742137. DOI: 10.1093/bioadv/vbaf001.

Spatially Resolved Multiomics: Data Analysis from Monoomics to Multiomics.

Huan C, Li J, Li Y, Zhao S, Yang Q, Zhang Z BME Front. 2025; 6():0084.

PMID: 39810754 PMC: 11725630. DOI: 10.34133/bmef.0084.

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