{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:30Z","timestamp":1772138070530,"version":"3.50.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,7]],"date-time":"2025-01-07T00:00:00Z","timestamp":1736208000000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The identification of biologically meaningful domains is a central step in the analysis of spatial transcriptomic data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Following Occam\u2019s razor, we show that a simple PCA-based algorithm for unsupervised spatial domain identification rivals the performance of ten competing state-of-the-art methods across six single-cell spatial transcriptomic datasets. Our reductionist approach, NichePCA, provides researchers with intuitive domain interpretation and excels in execution speed, robustness, and scalability.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The code is available at https:\/\/github.com\/imsb-uke\/nichepca.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf005","type":"journal-article","created":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T07:17:05Z","timestamp":1736147825000},"source":"Crossref","is-referenced-by-count":9,"title":["PCA-based spatial domain identification with state-of-the-art performance"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-8685-3263","authenticated-orcid":false,"given":"Darius P","family":"Schaub","sequence":"first","affiliation":[{"name":"Institute of Medical Systems Bioinformatics, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]},{"name":"III Department of Medicine, University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0995-2000","authenticated-orcid":false,"given":"Behnam","family":"Yousefi","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Bioinformatics, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]},{"name":"German Center for Child and Adolescent Health (DZKJ), Partner Site Hamburg, University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]}]},{"given":"Nico","family":"Kaiser","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Bioinformatics, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]},{"name":"III Department of Medicine, University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-5311-1718","authenticated-orcid":false,"given":"Robin","family":"Khatri","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Bioinformatics, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]}]},{"given":"Victor G","family":"Puelles","sequence":"additional","affiliation":[{"name":"III Department of Medicine, University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]},{"name":"Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]},{"name":"Department of Clinical Medicine, Aarhus University , Aarhus 8200,","place":["Denmark"]},{"name":"Department of Pathology, Aarhus University Hospital , Aarhus 8200,","place":["Denmark"]}]},{"given":"Christian F","family":"Krebs","sequence":"additional","affiliation":[{"name":"III Department of Medicine, University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]},{"name":"Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]},{"name":"Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]}]},{"given":"Ulf","family":"Panzer","sequence":"additional","affiliation":[{"name":"III Department of Medicine, University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]},{"name":"Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]},{"name":"Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4366-5662","authenticated-orcid":false,"given":"Stefan","family":"Bonn","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Bioinformatics, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]},{"name":"German Center for Child and Adolescent Health (DZKJ), Partner Site Hamburg, University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]},{"name":"Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]},{"name":"Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf , Hamburg 20246,","place":["Germany"]}]}],"member":"286","published-online":{"date-parts":[[2025,1,7]]},"reference":[{"key":"2025012508255281700_btaf005-B1","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1016\/j.cell.2022.12.010","article-title":"Molecular and spatial signatures of mouse brain aging at single-cell resolution","volume":"186","author":"Allen","year":"2023","journal-title":"Cell"},{"key":"2025012508255281700_btaf005-B2","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1186\/s13059-024-03241-7","article-title":"Library size confounds biology in spatial transcriptomics data","volume":"25","author":"Bhuva","year":"2024","journal-title":"Genome Biol"},{"key":"2025012508255281700_btaf005-B3","first-page":"406","author":"Cang","year":"2021"},{"key":"2025012508255281700_btaf005-B4","doi-asserted-by":"publisher","first-page":"aaa6090","DOI":"10.1126\/science.aaa6090","article-title":"Spatially resolved, highly multiplexed RNA profiling in single cells","volume":"348","author":"Chen","year":"2015","journal-title":"Science"},{"key":"2025012508255281700_btaf005-B5","doi-asserted-by":"publisher","first-page":"e22","DOI":"10.1093\/nar\/gkx1206","article-title":"Efficient in situ barcode sequencing using padlock probe-based BaristaSeq","volume":"46","author":"Chen","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2025012508255281700_btaf005-B6","doi-asserted-by":"publisher","first-page":"1739","DOI":"10.1038\/s41467-022-29439-6","article-title":"Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder","volume":"13","author":"Dong","year":"2022","journal-title":"Nat Commun"},{"key":"2025012508255281700_btaf005-B7","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1007\/s00213-008-1204-x","article-title":"Hippocampal SSTR4 somatostatin receptors control the selection of memory strategies","volume":"202","author":"Gastambide","year":"2009","journal-title":"Psychopharmacology (Berl)"},{"key":"2025012508255281700_btaf005-B8","doi-asserted-by":"publisher","first-page":"1342","DOI":"10.1038\/s41592-021-01255-8","article-title":"SpaGCN: integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network","volume":"18","author":"Hu","year":"2021","journal-title":"Nat Methods"},{"key":"2025012508255281700_btaf005-B9","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1186\/s13059-024-03361-0","article-title":"Benchmarking clustering, alignment, and integration methods for spatial transcriptomics","volume":"25","author":"Hu","year":"2024","journal-title":"Genome Biol"},{"key":"2025012508255281700_btaf005-B10","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1109\/TMI.2009.2035616","article-title":"Elastix: a toolbox for Intensity-Based medical image registration","volume":"29","author":"Klein","year":"2010","journal-title":"IEEE Trans Med Imaging"},{"key":"2025012508255281700_btaf005-B11","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat Methods"},{"key":"2025012508255281700_btaf005-B12","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1038\/s43588-022-00266-5","article-title":"Cell clustering for spatial transcriptomics data with graph neural networks","volume":"2","author":"Li","year":"2022","journal-title":"Nat Comput Sci"},{"key":"2025012508255281700_btaf005-B13","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1186\/s13059-022-02734-7","article-title":"BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies","volume":"23","author":"Li","year":"2022","journal-title":"Genome Biol"},{"key":"2025012508255281700_btaf005-B14","doi-asserted-by":"publisher","first-page":"100565","DOI":"10.1016\/j.xgen.2024.100565","article-title":"Complete spatially resolved gene expression is not necessary for identifying spatial domains","volume":"4","author":"Lin","year":"2024","journal-title":"Cell Genom"},{"key":"2025012508255281700_btaf005-B15","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1016\/j.csbj.2023.11.055","article-title":"A comprehensive overview of graph neural network-based approaches to clustering for spatial transcriptomics","volume":"23","author":"Liu","year":"2024","journal-title":"Comput Struct Biotechnol J"},{"key":"2025012508255281700_btaf005-B16","author":"Long","year":"2023"},{"key":"2025012508255281700_btaf005-B17","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1038\/s41467-023-36796-3","article-title":"Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST","volume":"14","author":"Long","year":"2023","journal-title":"Nat Commun"},{"key":"2025012508255281700_btaf005-B18","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.1038\/s41592-018-0229-2","article-title":"Deep generative modeling for single-cell transcriptomics","volume":"15","author":"Lopez","year":"2018","journal-title":"Nat Methods"},{"key":"2025012508255281700_btaf005-B19","doi-asserted-by":"publisher","author":"Maher","year":"2023","DOI":"10.1101\/2023.06.30.547258"},{"key":"2025012508255281700_btaf005-B20","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1126\/science.aau5324","article-title":"Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region","volume":"362","author":"Moffitt","year":"2018","journal-title":"Science"},{"key":"2025012508255281700_btaf005-B21","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1016\/j.cell.2012.12.026","article-title":"The ciliary G-protein-coupled receptor Gpr161 negatively regulates the sonic hedgehog pathway via cAMP signaling","volume":"152","author":"Mukhopadhyay","year":"2013","journal-title":"Cell"},{"key":"2025012508255281700_btaf005-B22","doi-asserted-by":"publisher","first-page":"1634","DOI":"10.1038\/s41592-022-01663-4","article-title":"Cellpose 2.0: how to train your own model","volume":"19","author":"Pachitariu","year":"2022","journal-title":"Nat Methods"},{"key":"2025012508255281700_btaf005-B23","doi-asserted-by":"publisher","first-page":"4076","DOI":"10.1038\/s41467-022-31739-w","article-title":"Identifying multicellular spatiotemporal organization of cells with SpaceFlow","volume":"13","author":"Ren","year":"2022","journal-title":"Nat Commun"},{"key":"2025012508255281700_btaf005-B24","doi-asserted-by":"publisher","first-page":"7203","DOI":"10.1038\/s41467-022-34879-1","article-title":"Spatially aware dimension reduction for spatial transcriptomics","volume":"13","author":"Shang","year":"2022","journal-title":"Nat Commun"},{"key":"2025012508255281700_btaf005-B25","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1038\/s41588-024-01664-3","article-title":"BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis","volume":"56","author":"Singhal","year":"2024","journal-title":"Nat Genet"},{"key":"2025012508255281700_btaf005-B26","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/s41592-020-01018-x","article-title":"Cellpose: a generalist algorithm for cellular segmentation","volume":"18","author":"Stringer","year":"2021","journal-title":"Nat Methods"},{"key":"2025012508255281700_btaf005-B27","doi-asserted-by":"publisher","first-page":"5233","DOI":"10.1038\/s41598-019-41695-z","article-title":"From Louvain to Leiden: guaranteeing well-connected communities","volume":"9","author":"Traag","year":"2019","journal-title":"Sci Rep"},{"key":"2025012508255281700_btaf005-B28","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1038\/s41588-023-01588-4","article-title":"CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity","volume":"56","author":"Varrone","year":"2024","journal-title":"Nat Genet"},{"key":"2025012508255281700_btaf005-B29","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1038\/s41587-023-01733-8","article-title":"The scverse project provides a computational ecosystem for single-cell omics data analysis","volume":"41","author":"Virshup","year":"2023","journal-title":"Nature Biotechnology"},{"key":"2025012508255281700_btaf005-B30","doi-asserted-by":"publisher","first-page":"936","DOI":"10.1016\/j.cell.2020.04.007","article-title":"The allen mouse brain common coordinate framework: a 3D reference atlas","volume":"181","author":"Wang","year":"2020","journal-title":"Cell"},{"key":"2025012508255281700_btaf005-B31","doi-asserted-by":"publisher","first-page":"eaat5691","DOI":"10.1126\/science.aat5691","article-title":"Three-dimensional intact-tissue sequencing of single-cell transcriptional states","volume":"361","author":"Wang","year":"2018","journal-title":"Science (New York, N.Y.)"},{"key":"2025012508255281700_btaf005-B32","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"},{"key":"2025012508255281700_btaf005-B33","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/s41467-023-44367-9","article-title":"MENDER: fast and scalable tissue structure identification in spatial omics data","volume":"15","author":"Yuan","year":"2024","journal-title":"Nat Commun"},{"key":"2025012508255281700_btaf005-B34","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1038\/s41592-024-02215-8","article-title":"Benchmarking spatial clustering methods with spatially resolved transcriptomics data","volume":"21","author":"Yuan","year":"2024","journal-title":"Nat Methods"},{"key":"2025012508255281700_btaf005-B35","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/s41586-023-06808-9","article-title":"Molecularly defined and spatially resolved cell atlas of the whole mouse brain","volume":"624","author":"Zhang","year":"2023","journal-title":"Nature"},{"key":"2025012508255281700_btaf005-B36","doi-asserted-by":"publisher","first-page":"1375","DOI":"10.1038\/s41587-021-00935-2","article-title":"Spatial transcriptomics at subspot resolution with BayesSpace","volume":"39","author":"Zhao","year":"2021","journal-title":"Nat Biotechnol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf005\/61370579\/btaf005.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/1\/btaf005\/61370579\/btaf005.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/1\/btaf005\/61370579\/btaf005.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,25]],"date-time":"2025-01-25T03:26:26Z","timestamp":1737775586000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf005\/7945104"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,12,26]]},"references-count":36,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,12,26]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf005","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.07.29.605550","asserted-by":"object"}]},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,1]]},"published":{"date-parts":[[2024,12,26]]},"article-number":"btaf005"}}