학술논문
SpatialData: an open and universal data framework for spatial omics
Document Type
Article
Author
Marconato, Luca; Palla, Giovanni; Yamauchi, Kevin A.; Virshup, Isaac; Heidari, Elyas; Treis, Tim; Vierdag, Wouter-Michiel; Toth, Marcella; Stockhaus, Sonja; Shrestha, Rahul B.; Rombaut, Benjamin; Pollaris, Lotte; Lehner, Laurens; Vöhringer, Harald; Kats, Ilia; Saeys, Yvan; Saka, Sinem K.; Huber, Wolfgang; Gerstung, Moritz; Moore, Josh; Theis, Fabian J.; Stegle, Oliver
Source
Nature Methods; 20240101, Issue: Preprints p1-5, 5p
Subject
Language
ISSN
15487091; 15487105
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.