ArticleNature methods2025
SpatialData: an open and universal data framework for spatial omics.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 141 papers, 3 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
141 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Mass spectrometry-based human spatial omics: fundamentals, innovations, and applications.Journal of biomedical science · 2026Pooled it
- Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective.Briefings in bioinformatics · 2025Pooled it
- Driving innovations in cancer research through spatial metabolomics: a bibliometric review of trends and hotspot.Frontiers in immunology · 2025Pooled it
- The genesis of cutaneous neurogenic inflammation is a multi-step process requiring dendritic cell aggregation.Immunity · 2026Article
- Single-cell and spatial transcriptomics define eosinophil heterogeneity during influenza A virus-induced exacerbation of fungal allergic asthma in C57BL/6 mice.Journal of leukocyte biology · 2026Article
- Multi-stromal organoid co-culture modelling reveals epithelial-fibroblast heterogeneity in pancreatic cancer and pancreatitis.Nature cell biology · 2026Article
- Integrated Multi-Omics Reveals Cellular States and Microenvironmental Remodeling in Coexisting DCIS and IDC.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- HESTIA: scalable multimodal integration of histology and high-resolution spatial Transcriptomics for robust spatial domain identification.Briefings in bioinformatics · 2026Article
- Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.Nature methods · 2026Article
- Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis.Nature genetics · 2026Article
- Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering.Nature methods · 2026Article
- DeepPathway: predicting pathway expression from histopathology images.Bioinformatics (Oxford, England) · 2026Article
- HuBMAP Data Portal: a resource for multimodal spatial and single-cell data of healthy human tissues.ArXiv · 2026Article
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- MuSpAn: a toolbox for multiscale spatial analysis.Nature communications · 2026Article
- SpatioTemporal Omics Consortium: a global effort for biological discovery across species, space and time.Nature methods · 2026Article
- Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data.Nature methods · 2026Article
- Integrative spatial multi-omics reveals the tumor ecosystem: From mechanistic insights to therapeutic strategies.iScience · 2026Review
- Multimodal spatial omics: From data acquisition to computational integration.Patterns (New York, N.Y.) · 2026Review
- LYNX: a deep generative model for linking spatial dynamics and cell interactions in multimodal spatial data.bioRxiv : the preprint server for biology · 2026Article
81 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.