{"id":"https://openalex.org/W7214013740","doi":"https://doi.org/10.1371/journal.pcbi.1014041","title":"OT-knn: A neighborhood-aware optimal transport framework for aligning spatial transcriptomics data","display_name":"OT-knn: A neighborhood-aware optimal transport framework for aligning spatial transcriptomics data","publication_year":2026,"publication_date":"2026-09-22","ids":{"openalex":"https://openalex.org/W7214013740","doi":"https://doi.org/10.1371/journal.pcbi.1014041","pmid":"https://pubmed.ncbi.nlm.nih.gov/42771689","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13641709"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1014041","doi":"https://doi.org/10.1371/journal.pcbi.1014041","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1014041","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1014041&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1014041&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109514020","display_name":"Jia Song","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jia Song","raw_affiliation_strings":["The Pennsylvania State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pennsylvania State University","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5125010244","display_name":"Qunhua Li","orcid":"https://orcid.org/0000-0003-0675-7648","observed_orcids":["https://orcid.org/0000-0003-0675-7648"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Qunhua Li","raw_affiliation_strings":["The Pennsylvania State University"],"raw_orcid":"https://orcid.org/0000-0003-0675-7648","affiliations":[{"raw_affiliation_string":"The Pennsylvania State University","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5125010244"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":{"value":3043,"currency":"USD","value_usd":3043},"apc_paid":{"value":3043,"currency":"USD","value_usd":3043},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.57230522,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"9","first_page":"e1014041","last_page":"e1014041"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/spatial-transcriptomics","display_name":"spatial transcriptomics","score":0.9890000224113464},{"id":"https://openalex.org/keywords/optimal-transport","display_name":"optimal transport","score":0.9079999923706055},{"id":"https://openalex.org/keywords/k-nearest-neighbors","display_name":"k-nearest neighbors","score":0.9409999847412109},{"id":"https://openalex.org/keywords/spatial-deformation","display_name":"spatial deformation","score":0.6449999809265137},{"id":"https://openalex.org/keywords/cross-platform-comparison","display_name":"cross-platform comparison","score":0.5910000205039978},{"id":"https://openalex.org/keywords/brain-development","display_name":"brain development","score":0.5180000066757202},{"id":"https://openalex.org/keywords/brain-aging","display_name":"brain aging","score":0.8840000033378601},{"id":"https://openalex.org/keywords/dorsolateral-prefrontal-cortex","display_name":"dorsolateral prefrontal cortex","score":0.9020000100135803},{"id":"https://openalex.org/keywords/mouse-embryo","display_name":"mouse embryo","score":0.7699999809265137},{"id":"https://openalex.org/keywords/tissue-microenvironment","display_name":"tissue microenvironment","score":0.5040000081062317}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6920999884605408},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6337000131607056},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.532800018787384},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5223000049591064},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.45989999175071716},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.4577000141143799},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.45750001072883606},{"id":"https://openalex.org/C64754055","wikidata":"https://www.wikidata.org/wiki/Q7574053","display_name":"Spatial contextual awareness","level":2,"score":0.4562000036239624},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4011000096797943},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3944999873638153},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.35839998722076416},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3174999952316284},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.3116999864578247},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3084999918937683},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.30640000104904175},{"id":"https://openalex.org/C158709400","wikidata":"https://www.wikidata.org/wiki/Q3578586","display_name":"Spatial ecology","level":2,"score":0.29820001125335693},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.295199990272522},{"id":"https://openalex.org/C2780508717","wikidata":"https://www.wikidata.org/wiki/Q72788","display_name":"Dorsolateral prefrontal cortex","level":4,"score":0.28870001435279846},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.2639000117778778},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.2578999996185303},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.2533000111579895},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.2508000135421753}],"mesh":[{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1014041","doi":"https://doi.org/10.1371/journal.pcbi.1014041","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1014041","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1014041&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"doi:10.64898/2026.02.19.706743","doi":"https://doi.org/10.64898/2026.02.19.706743","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.02.19.706743","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:13641709","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13641709/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13641709/pdf/pcbi.1014041.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmid:42771689","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42771689","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:3fa20814ee744b30b82aaf97fa240e4b","doi":null,"is_oa":false,"landing_page_url":"https://doaj.org/article/3fa20814ee744b30b82aaf97fa240e4b","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 22, Iss 9, p e1014041 (2026)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1014041","doi":"https://doi.org/10.1371/journal.pcbi.1014041","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1014041","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1014041&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1846817163","display_name":"Statistical methods for improving reproducibility and utility of chromatin interaction data","funder_award_id":"R01GM109453","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G9000371764","display_name":null,"funder_award_id":"R01 GM109453","funder_id":"https://openalex.org/F4320306080","funder_display_name":"Foundation for the National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306080","display_name":"Foundation for the National Institutes of Health","ror":"https://ror.org/00k86s890"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7214013740.pdf","grobid_xml":"https://content.openalex.org/works/W7214013740.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1503727145","https://openalex.org/W2042789810","https://openalex.org/W2143668817","https://openalex.org/W2471536144","https://openalex.org/W2533012945","https://openalex.org/W2808465642","https://openalex.org/W2889453805","https://openalex.org/W2915848182","https://openalex.org/W2923300855","https://openalex.org/W2963469388","https://openalex.org/W2969906472","https://openalex.org/W2972757028","https://openalex.org/W2999977864","https://openalex.org/W3036371598","https://openalex.org/W3037329734","https://openalex.org/W3112563877","https://openalex.org/W3119671877","https://openalex.org/W3126958162","https://openalex.org/W3196495189","https://openalex.org/W3205213119","https://openalex.org/W3214755680","https://openalex.org/W4226106494","https://openalex.org/W4229021644","https://openalex.org/W4229033508","https://openalex.org/W4242111955","https://openalex.org/W4280494993","https://openalex.org/W4294042823","https://openalex.org/W4306194402","https://openalex.org/W4313312704","https://openalex.org/W4385955242","https://openalex.org/W4388530027","https://openalex.org/W4389481214","https://openalex.org/W4404349303","https://openalex.org/W4406867208","https://openalex.org/W4411670013","https://openalex.org/W4415795699"],"related_works":["https://openalex.org/W4389481214","https://openalex.org/W4280494993","https://openalex.org/W7154472548","https://openalex.org/W7143468608","https://openalex.org/W7139967614","https://openalex.org/W7148461950","https://openalex.org/W4387579820","https://openalex.org/W4406867208","https://openalex.org/W4387580076","https://openalex.org/W4411081312"],"abstract_inverted_index":{"Abstract":[0],"Spatial":[1,208],"transcriptomics":[2,209],"(ST)":[3],"measures":[4,215],"gene":[5,216,251,349],"expression":[6],"while":[7,218],"preserving":[8],"spatial":[9,82,178,348],"context":[10,88],"within":[11,64,194],"tissues,":[12],"enabling":[13],"detailed":[14],"characterization":[15],"of":[16,177,221,279,302,347],"tissue":[17,26,235,276,304,321],"organization.":[18],"As":[19],"ST":[20,57,123],"technologies":[21],"advance,":[22],"aligning":[23],"datasets":[24,120,158,333],"across":[25,261,275,351],"sections,":[27],"individuals,":[28,238],"platforms,":[29,124],"and":[30,46,95,118,141,151,162,170,184,204,256,299,305,331,337,360],"developmental":[31,182],"stages":[32],"has":[33],"become":[34],"increasingly":[35],"important":[36,197],"but":[37],"remains":[38],"challenging":[39],"due":[40],"to":[41,93,102,206,270,309],"sparse":[42],"expression,":[43,75],"biological":[44,258],"heterogeneity,":[45,181],"geometric":[47],"distortions":[48],"between":[49,106],"slices.":[50,107,277],"We":[51,108,324],"introduce":[52],"OT-knn,":[53],"a":[54,145,152,211,268,296],"method":[55,269,327],"for":[56,198],"alignment":[58,117],"that":[59,89,214],"integrates":[60],"local":[61],"neighborhood":[62],"information":[63,289],"an":[65],"optimal":[66],"transport":[67],"framework.":[68],"Rather":[69],"than":[70],"relying":[71],"solely":[72],"on":[73,328],"single-spot":[74],"OT-knn":[76,110,167],"reconstructs":[77],"each":[78,223,282],"spot":[79],"using":[80,111,155],"its":[81,291],"k":[83],"-nearest":[84],"neighbors,":[85],"capturing":[86],"microenvironment":[87],"is":[90,196,210,243],"more":[91,297,344],"robust":[92,171],"noise":[94],"variability.":[96],"These":[97],"representations":[98],"are":[99,192,317],"then":[100],"used":[101],"derive":[103],"probabilistic":[104],"correspondences":[105],"evaluate":[109],"simulated":[112,330],"data":[113,130,137,232,316],"with":[114,138],"known":[115],"ground-truth":[116],"real":[119,332],"from":[121,226,233,290,334],"multiple":[122],"including":[125],"human":[126],"dorsolateral":[127],"prefrontal":[128],"cortex":[129],"(10x":[131],"Genomics":[132],"Visium),":[133],"mouse":[134,156],"brain":[135,148,339],"aging":[136],"both":[139,329],"within-donor":[140],"cross-donor":[142],"comparisons":[143,346],"(MERFISH),":[144],"multi-stage":[146],"axolotl":[147,338],"dataset":[149],"(Stereo-seq),":[150],"cross-platform":[153],"analysis":[154],"embryo":[157],"profiled":[159],"by":[160,284],"Stereo-seq":[161],"seqFISH.":[163],"Across":[164],"these":[165],"settings,":[166],"achieves":[168],"accurate":[169],"alignment,":[172],"particularly":[173],"in":[174,227],"the":[175,228,303,315,320],"presence":[176],"deformation,":[179],"donor":[180],"variation":[183],"technological":[185],"differences.":[186],"Author":[187],"summary":[188],"Understanding":[189],"how":[190,200],"cells":[191],"arranged":[193],"tissues":[195],"studying":[199],"organs":[201],"develop,":[202],"age,":[203],"respond":[205],"disease.":[207,361],"new":[212],"technology":[213],"activity":[217,350],"keeping":[219],"track":[220],"where":[222],"measurement":[224],"comes":[225],"tissue.":[229],"However,":[230],"comparing":[231],"different":[234,237,240],"slices,":[236],"or":[239,319],"time":[241],"points":[242],"difficult.":[244],"Tissues":[245],"can":[246,253,354],"change":[247],"shape":[248],"during":[249],"preparation,":[250],"measurements":[252],"be":[254],"noisy,":[255],"natural":[257],"differences":[259],"exist":[260],"samples.":[262],"In":[263],"this":[264],"work,":[265],"we":[266,286],"develop":[267],"better":[271],"match":[272,310],"corresponding":[273],"regions":[274],"Instead":[278],"looking":[280],"at":[281],"location":[283],"itself,":[285],"also":[287],"consider":[288],"surrounding":[292],"neighborhood.":[293],"This":[294],"provides":[295],"stable":[298],"informative":[300],"view":[301],"makes":[306],"it":[307],"easier":[308],"similar":[311],"regions,":[312],"even":[313],"when":[314],"imperfect":[318],"shapes":[322],"differ.":[323],"test":[325],"our":[326],"human,":[335],"mouse,":[336],"tissues.":[340],"Our":[341],"approach":[342],"enables":[343],"reliable":[345],"samples,":[352],"which":[353],"help":[355],"researchers":[356],"study":[357],"development,":[358],"aging,":[359]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-09-23T00:00:00"}