{"doi":"10.1038/s41592-024-02212-x","title":"SpatialData: an open and universal data framework for spatial omics","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.","journal":"Nature Methods","year":2024,"id":9931,"datarank":2.725279068839891,"base_score":5.159055299214529,"endowment":5.159055299214529,"self_citation_contribution":0.7738582948821795,"citation_network_contribution":1.9514207739577116,"self_endowment_contribution":0.7738582948821795,"citer_contribution":1.9514207739577116,"corpus_percentile":null,"corpus_rank":null,"citation_count":173,"citer_count":153,"citers_with_citation_signal":94,"citers_with_endowment":94,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.1897,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-03-20","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":3564,"name":"Giovanni Palla","orcid":"0000-0002-8004-4462","position":1,"is_corresponding":false},{"id":39830,"name":"Kevin A. Yamauchi","orcid":"0000-0002-7818-1388","position":2,"is_corresponding":false},{"id":3582,"name":"Valeh Valiollah Pour Amiri","orcid":"0000-0002-2008-5297","position":3,"is_corresponding":false},{"id":39831,"name":"Elyas Heidari","orcid":"0000-0002-6004-3999","position":4,"is_corresponding":false},{"id":35697,"name":"Tim Treis","orcid":"0000-0002-9686-4799","position":5,"is_corresponding":false},{"id":85042,"name":"Wouter-Michiel Vierdag","orcid":"0000-0003-1666-5421","position":6,"is_corresponding":false},{"id":39832,"name":"Marcella Toth","orcid":"0009-0002-0685-8852","position":7,"is_corresponding":false},{"id":85043,"name":"Sonja Stockhaus","orcid":"0009-0005-7712-8154","position":8,"is_corresponding":false},{"id":39833,"name":"Rahul B. Shrestha","orcid":"0000-0002-6429-4402","position":9,"is_corresponding":false},{"id":85044,"name":"Benjamin Rombaut","orcid":"0000-0002-4022-715X","position":10,"is_corresponding":false},{"id":85045,"name":"Lotte Pollaris","orcid":"0000-0002-9509-9386","position":11,"is_corresponding":false},{"id":85046,"name":"Laurens Lehner","orcid":"0000-0001-7690-7168","position":12,"is_corresponding":false},{"id":39834,"name":"Harald Vöhringer","orcid":"0000-0003-2513-4518","position":13,"is_corresponding":false},{"id":3567,"name":"Ilia Kats","orcid":"0000-0001-5220-5671","position":14,"is_corresponding":false},{"id":49005,"name":"Yvan Saeys","orcid":"0000-0002-0415-1506","position":15,"is_corresponding":false},{"id":85047,"name":"Sinem K. Saka","orcid":"0000-0002-5017-379X","position":16,"is_corresponding":false},{"id":37159,"name":"Keegan Korthauer","orcid":"0000-0002-4565-1654","position":17,"is_corresponding":false},{"id":13484,"name":"Moritz Gerstung","orcid":"0000-0001-6709-963X","position":18,"is_corresponding":false},{"id":39835,"name":"Josh Moore","orcid":"0000-0003-4028-811X","position":19,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":20,"is_corresponding":false},{"id":3589,"name":"Oliver Stegle","orcid":"0000-0002-8818-7193","position":21,"is_corresponding":false},{"id":39829,"name":"Luca Marconato","orcid":"0000-0003-3198-1326","position":0,"is_corresponding":true}],"reference_count":36,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}