{"doi":"10.1101/2023.05.05.539647","title":"SpatialData: an open and universal data framework for spatial omics","abstract":"Spatially resolved omics technologies are transforming our understanding of biological tissues. However, handling uni- and multi-modal spatial omics datasets remains a challenge owing to large volumes of data, heterogeneous data types and the lack of unified spatially-aware data structures. Here, we introduce SpatialData, a framework that establishes a unified and extensible multi-platform 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 via multiple vignettes, including integrative analysis on a multi-modal Xenium and Visium breast cancer study.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":3946,"datarank":1.2602039005963976,"base_score":3.4965075614664802,"endowment":3.4965075614664802,"self_citation_contribution":0.5244761342199721,"citation_network_contribution":0.7357277663764255,"self_endowment_contribution":0.5244761342199721,"citer_contribution":0.7357277663764255,"corpus_percentile":null,"corpus_rank":null,"citation_count":32,"citer_count":27,"citers_with_citation_signal":22,"citers_with_endowment":22,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.231,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-05-08","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":39832,"name":"Marcella Toth","orcid":"0009-0002-0685-8852","position":6,"is_corresponding":false},{"id":39833,"name":"Rahul B. Shrestha","orcid":"0000-0002-6429-4402","position":7,"is_corresponding":false},{"id":39834,"name":"Harald Vöhringer","orcid":"0000-0003-2513-4518","position":8,"is_corresponding":false},{"id":37159,"name":"Keegan Korthauer","orcid":"0000-0002-4565-1654","position":9,"is_corresponding":false},{"id":13484,"name":"Moritz Gerstung","orcid":"0000-0001-6709-963X","position":10,"is_corresponding":false},{"id":39835,"name":"Josh Moore","orcid":"0000-0003-4028-811X","position":11,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":12,"is_corresponding":false},{"id":3589,"name":"Oliver Stegle","orcid":"0000-0002-8818-7193","position":13,"is_corresponding":false},{"id":39829,"name":"Luca Marconato","orcid":"0000-0003-3198-1326","position":0,"is_corresponding":true}],"reference_count":43,"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":[]}