2024/03/20 by Luca Marconato, Giovanni Palla, Kevin A. Yamauchi +19 · 1 voice
Biochemistry, Genetics and Molecular Biology · #Single-cell and spatial transcriptomics #Gene expression and cancer classification #Bioinformatics and Genomic Networks
paper · pdf · doi:10.1038/s41592-024-02212-x
openalex publication_date 2024/03/20 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/03
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.