{"doi":"10.1101/2025.01.13.632601","title":"2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices","abstract":"Imaging-based spatially resolved transcriptomics can localize transcripts within tissue sections in 3D. Cell segmentation assigns transcripts to cells and precedes annotation of cell function. However, cell segmentation is usually performed in 2D, thus unable to deal with spatial doublets arising from overlapping cells, resulting in segmented cells containing transcripts originating from multiple cell types. Here we present a computational tool called ovrlpy that identifies overlapping cells, tissue folds, and inaccurate cell-segmentation by analyzing transcript localization in 3D.","journal":null,"year":2025,"id":6286,"datarank":0.48566181076739434,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.17374557951541894,"self_endowment_contribution":0.31191623125197543,"citer_contribution":0.17374557951541894,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":5,"citers_with_citation_signal":4,"citers_with_endowment":4,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0513,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-15","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":58468,"name":"Niklas Müller-Bötticher","orcid":"0000-0001-5103-7282","position":1,"is_corresponding":false},{"id":58469,"name":"Alexander Malt","orcid":null,"position":2,"is_corresponding":false},{"id":58470,"name":"Leyao Ma","orcid":null,"position":3,"is_corresponding":false},{"id":58472,"name":"Paul Kiessling","orcid":null,"position":5,"is_corresponding":false},{"id":58473,"name":"Paul Horn","orcid":"0000-0002-8755-7703","position":6,"is_corresponding":false},{"id":544,"name":"Adrien Guillot","orcid":"0000-0002-6002-9986","position":7,"is_corresponding":false},{"id":58474,"name":"Louis Benedikt Kuemmerle","orcid":"0000-0002-9193-1243","position":8,"is_corresponding":false},{"id":569,"name":"Frank Tacke","orcid":"0000-0001-6206-0226","position":9,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":10,"is_corresponding":false},{"id":15530,"name":"Christoph Kuppe","orcid":"0000-0003-4597-9833","position":11,"is_corresponding":false},{"id":13430,"name":"Roland Eils","orcid":"0000-0002-0034-4036","position":13,"is_corresponding":false},{"id":13428,"name":"Anna Ehinger","orcid":"0000-0001-9225-7396","position":14,"is_corresponding":false},{"id":58477,"name":"Naveed Ishaque","orcid":"0000-0002-8426-901X","position":15,"is_corresponding":false},{"id":27707,"name":"Sergio Marco Salas","orcid":"0000-0002-4636-0322","position":16,"is_corresponding":false},{"id":58478,"name":"Paul Kießling","orcid":"0000-0002-9794-9532","position":17,"is_corresponding":false},{"id":24364,"name":"Louis Kümmerle","orcid":null,"position":18,"is_corresponding":false},{"id":58479,"name":"L.L. Ma","orcid":"0009-0005-5029-7476","position":19,"is_corresponding":false},{"id":24374,"name":"Mats Nilsson","orcid":"0000-0001-9985-0387","position":20,"is_corresponding":false},{"id":58467,"name":"Sebastian Tiesmeyer","orcid":"0000-0002-0492-1523","position":0,"is_corresponding":true}],"reference_count":18,"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":[]}