{"id":"https://openalex.org/W7162314761","doi":"https://doi.org/10.1093/bib/bbag255","title":"A comprehensive survey of computer vision methods for spatial transcriptomics","display_name":"A comprehensive survey of computer vision methods for spatial transcriptomics","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7162314761","doi":"https://doi.org/10.1093/bib/bbag255","pmid":"https://pubmed.ncbi.nlm.nih.gov/42184118"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag255","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag255","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbag255","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5136914228","display_name":"Junchao Zhu","orcid":"https://orcid.org/0000-0001-6610-9808"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junchao Zhu","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,"],"raw_orcid":"https://orcid.org/0000-0001-6610-9808","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037133367","display_name":"Ruining Deng","orcid":"https://orcid.org/0000-0001-6300-8518"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruining Deng","raw_affiliation_strings":["Weill Cornell Medicine , 1300 York Ave, New York, NY 10065,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Weill Cornell Medicine , 1300 York Ave, New York, NY 10065,","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136958570","display_name":"Junlin Guo","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junlin Guo","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064015426","display_name":"Tianyuan Yao","orcid":"https://orcid.org/0000-0002-1848-079X"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tianyuan Yao","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102978740","display_name":"Siqi Lu","orcid":"https://orcid.org/0000-0002-8061-8120"},"institutions":[{"id":"https://openalex.org/I16285277","display_name":"William & Mary","ror":"https://ror.org/03hsf0573","country_code":"US","type":"education","lineage":["https://openalex.org/I16285277"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Siqi Lu","raw_affiliation_strings":["Department of Computer Science, The College of William and Mary , 200 Stadium Drive, Williamsburg, VA 23185,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The College of William and Mary , 200 Stadium Drive, Williamsburg, VA 23185,","institution_ids":["https://openalex.org/I16285277"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102765244","display_name":"Chongyu Qu","orcid":"https://orcid.org/0009-0008-8893-2748"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chongyu Qu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111152727","display_name":"Juming Xiong","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Juming Xiong","raw_affiliation_strings":["Department of Electrical and Computer Engineering , Vanderbilt University, 2301 Vanderbilt Place, Nashville, TN 37235,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering , Vanderbilt University, 2301 Vanderbilt Place, Nashville, TN 37235,","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121274183","display_name":"Yanfan Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yanfan Zhu","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110162244","display_name":"Zhengyi Lu","orcid":"https://orcid.org/0009-0003-4723-7187"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhengyi Lu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101259625","display_name":"Yuechen Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuechen Yang","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113473288","display_name":"Marilyn Lionts","orcid":"https://orcid.org/0000-0002-9889-3390"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marilyn Lionts","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136902931","display_name":"Yucheng Tang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210127875","display_name":"Nvidia (United States)","ror":"https://ror.org/03jdj4y14","country_code":"US","type":"company","lineage":["https://openalex.org/I4210127875"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yucheng Tang","raw_affiliation_strings":["NVIDIA, 2788 San Tomas Expressway , Santa Clara, CA 95051,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NVIDIA, 2788 San Tomas Expressway , Santa Clara, CA 95051,","institution_ids":["https://openalex.org/I4210127875"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052339079","display_name":"Daguang Xu","orcid":"https://orcid.org/0000-0002-4621-881X"},"institutions":[{"id":"https://openalex.org/I4210127875","display_name":"Nvidia (United States)","ror":"https://ror.org/03jdj4y14","country_code":"US","type":"company","lineage":["https://openalex.org/I4210127875"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daguang Xu","raw_affiliation_strings":["NVIDIA, 2788 San Tomas Expressway , Santa Clara, CA 95051,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NVIDIA, 2788 San Tomas Expressway , Santa Clara, CA 95051,","institution_ids":["https://openalex.org/I4210127875"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136917171","display_name":"Yu Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu Wang","raw_affiliation_strings":["Department of Biostatistics, Vanderbilt University Medical Center , 2525 West End Avenue, Nashville, TN 37203,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Vanderbilt University Medical Center , 2525 West End Avenue, Nashville, TN 37203,","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136901152","display_name":"Shilin Zhao","orcid":"https://orcid.org/0000-0002-3921-3965"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shilin Zhao","raw_affiliation_strings":["Department of Biostatistics, Vanderbilt University Medical Center , 2525 West End Avenue, Nashville, TN 37203,"],"raw_orcid":"https://orcid.org/0000-0002-3921-3965","affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Vanderbilt University Medical Center , 2525 West End Avenue, Nashville, TN 37203,","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136937580","display_name":"Haichun Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haichun Yang","raw_affiliation_strings":["Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center , 1161 21st Avenue South, Nashville, TN 37232,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center , 1161 21st Avenue South, Nashville, TN 37232,","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5136957289","display_name":"Yuankai Huo","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuankai Huo","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","Department of Electrical and Computer Engineering, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","institution_ids":["https://openalex.org/I200719446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5136957289"],"corresponding_institution_ids":["https://openalex.org/I200719446"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.58057832,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.995199978351593,"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":0.995199978351593,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.001500000013038516,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.0008999999845400453,"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/key","display_name":"Key (lock)","score":0.5407000184059143},{"id":"https://openalex.org/keywords/tracing","display_name":"Tracing","score":0.5170000195503235},{"id":"https://openalex.org/keywords/perspective","display_name":"Perspective (graphical)","score":0.501800000667572},{"id":"https://openalex.org/keywords/virtual-reality","display_name":"Virtual reality","score":0.3479999899864197},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.335099995136261},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.3003000020980835}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6898000240325928},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5407000184059143},{"id":"https://openalex.org/C138673069","wikidata":"https://www.wikidata.org/wiki/Q322229","display_name":"Tracing","level":2,"score":0.5170000195503235},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5095999836921692},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5080000162124634},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.501800000667572},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.3504999876022339},{"id":"https://openalex.org/C194969405","wikidata":"https://www.wikidata.org/wiki/Q170519","display_name":"Virtual reality","level":2,"score":0.3479999899864197},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.335099995136261},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.31310001015663147},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.3003000020980835},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.28360000252723694},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.27480000257492065},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.26669999957084656},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.2574000060558319},{"id":"https://openalex.org/C3019007443","wikidata":"https://www.wikidata.org/wiki/Q568742","display_name":"3d model","level":2,"score":0.25029999017715454}],"mesh":[{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag255","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag255","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42184118","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42184118","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,"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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13200551","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13200551/","pdf_url":null,"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,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag255","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag255","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6686806082725525,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1296419534","display_name":null,"funder_award_id":"G-1903-03793","funder_id":"https://openalex.org/F4320309446","funder_display_name":"Leona M. and Harry B. Helmsley Charitable Trust"},{"id":"https://openalex.org/G1985087239","display_name":null,"funder_award_id":"R01EB033385","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2587922514","display_name":null,"funder_award_id":"REB017230","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3196715191","display_name":"NSF Convergence Accelerator Track D: Scalable, TRaceable Ai for Imaging Translation: Innovation to Implementation for Accelerated Impact (STRAIT I3)","funder_award_id":"2040462","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G398763758","display_name":null,"funder_award_id":"R01DK135597","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5076521518","display_name":null,"funder_award_id":"R01DK132338","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6493331838","display_name":null,"funder_award_id":"R01MH125931","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6573109839","display_name":null,"funder_award_id":"G-2103-05128","funder_id":"https://openalex.org/F4320309446","funder_display_name":"Leona M. and Harry B. Helmsley Charitable Trust"},{"id":"https://openalex.org/G8120692442","display_name":"CPS: Medium: iCMS: Intelligent Cyber Microscopy System for Long-term Microscope Imaging","funder_award_id":"2434229","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309446","display_name":"Leona M. and Harry B. Helmsley Charitable Trust","ror":"https://ror.org/011x6n313"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":108,"referenced_works":["https://openalex.org/W2194775991","https://openalex.org/W2471536144","https://openalex.org/W2516809705","https://openalex.org/W2923300855","https://openalex.org/W2937443931","https://openalex.org/W2952459265","https://openalex.org/W2972445800","https://openalex.org/W2972983657","https://openalex.org/W2996171578","https://openalex.org/W2999977864","https://openalex.org/W3021920958","https://openalex.org/W3036371598","https://openalex.org/W3036882247","https://openalex.org/W3046305306","https://openalex.org/W3108118546","https://openalex.org/W3119379269","https://openalex.org/W3126958162","https://openalex.org/W3133711868","https://openalex.org/W3165120573","https://openalex.org/W3190202966","https://openalex.org/W3205213119","https://openalex.org/W3213918788","https://openalex.org/W3214280461","https://openalex.org/W4220765701","https://openalex.org/W4220897949","https://openalex.org/W4226192560","https://openalex.org/W4280494993","https://openalex.org/W4283704002","https://openalex.org/W4285803722","https://openalex.org/W4306845387","https://openalex.org/W4309918428","https://openalex.org/W4317936159","https://openalex.org/W4319299885","https://openalex.org/W4360999347","https://openalex.org/W4384023988","https://openalex.org/W4384816663","https://openalex.org/W4386031249","https://openalex.org/W4386789742","https://openalex.org/W4387211696","https://openalex.org/W4387259074","https://openalex.org/W4387439135","https://openalex.org/W4387808846","https://openalex.org/W4388830671","https://openalex.org/W4389455629","https://openalex.org/W4389938094","https://openalex.org/W4390189873","https://openalex.org/W4390242455","https://openalex.org/W4390872297","https://openalex.org/W4391528171","https://openalex.org/W4392168151","https://openalex.org/W4392393203","https://openalex.org/W4392947532","https://openalex.org/W4394758412","https://openalex.org/W4394870153","https://openalex.org/W4394894190","https://openalex.org/W4394927236","https://openalex.org/W4399041754","https://openalex.org/W4399369150","https://openalex.org/W4399388318","https://openalex.org/W4399554368","https://openalex.org/W4399863709","https://openalex.org/W4399970333","https://openalex.org/W4400519842","https://openalex.org/W4401317959","https://openalex.org/W4401450053","https://openalex.org/W4402660143","https://openalex.org/W4402733572","https://openalex.org/W4403394014","https://openalex.org/W4403853489","https://openalex.org/W4404135221","https://openalex.org/W4404139282","https://openalex.org/W4404349892","https://openalex.org/W4404918820","https://openalex.org/W4405409648","https://openalex.org/W4405461799","https://openalex.org/W4405596115","https://openalex.org/W4406260087","https://openalex.org/W4406870564","https://openalex.org/W4407360292","https://openalex.org/W4407912844","https://openalex.org/W4408414133","https://openalex.org/W4409488923","https://openalex.org/W4410701189","https://openalex.org/W4411186225","https://openalex.org/W4411279214","https://openalex.org/W4411415215","https://openalex.org/W4411421751","https://openalex.org/W4412006463","https://openalex.org/W4412065395","https://openalex.org/W4412929290","https://openalex.org/W4412953754","https://openalex.org/W4413147041","https://openalex.org/W4413270570","https://openalex.org/W4413356115","https://openalex.org/W4413412913","https://openalex.org/W4414003039","https://openalex.org/W4414081644","https://openalex.org/W4414364902","https://openalex.org/W4414484426","https://openalex.org/W4414531149","https://openalex.org/W4416292771","https://openalex.org/W4416688141","https://openalex.org/W4417164932","https://openalex.org/W7118182048","https://openalex.org/W7124445117","https://openalex.org/W7127174287","https://openalex.org/W7136318156","https://openalex.org/W7137992141"],"related_works":[],"abstract_inverted_index":{"Spatial":[0],"transcriptomics":[1],"(ST)":[2],"enables":[3],"the":[4,37,60,166,183],"simultaneous":[5],"measurement":[6],"of":[7,36,62,108,122,169,187,237],"gene":[8],"expression":[9],"and":[10,23,52,66,91,117,172,202,204,213,223,231],"spatial":[11,45,175],"localization":[12],"within":[13,42],"tissue":[14,21,163],"sections,":[15],"providing":[16],"unprecedented":[17],"opportunities":[18],"to":[19,50,94,103,226],"dissect":[20],"architecture":[22],"functional":[24],"organization.":[25],"As":[26],"a":[27,217],"relatively":[28],"new":[29,80],"omics":[30,176],"technology,":[31],"bioinformatics":[32,84],"has":[33],"driven":[34],"much":[35],"innovation":[38],"in":[39,71],"ST.":[40],"However,":[41],"these":[43],"frameworks,":[44],"information":[46],"is":[47,241],"often":[48],"reduced":[49],"locations":[51],"relationships":[53],"between":[54],"molecular":[55,95,149],"profiles,":[56],"without":[57],"fully":[58],"leveraging":[59],"wealth":[61],"sub-micron":[63],"morphological":[64,144],"detail":[65],"histological":[67,89],"knowledge":[68],"available.":[69],"Advances":[70],"computer":[72,156,188],"vision-based":[73],"artificial":[74],"intelligence":[75],"(AI)":[76],"are":[77],"opening":[78],"exciting":[79],"avenues":[81],"beyond":[82],"conventional":[83],"approaches":[85,196],"by":[86],"modeling":[87],"complex":[88],"patterns":[90],"linking":[92],"morphology":[93],"states.":[96],"More":[97],"excitingly,":[98],"they":[99],"bring":[100],"fresh":[101],"perspectives":[102],"potentially":[104],"address":[105],"key":[106,211],"limitations":[107],"ST,":[109],"including":[110],"its":[111,224],"high":[112],"cost,":[113],"limited":[114],"clinical":[115,153,232],"applicability,":[116],"reliance":[118],"on":[119,220],"2D":[120,170],"analysis":[121],"inherently":[123],"3D":[124,162,174],"tissues.":[125],"For":[126],"instance,":[127],"models":[128,191],"that":[129],"predict":[130],"ST":[131,193,222,239],"directly":[132],"from":[133,146],"histology":[134],"images":[135],"enable":[136],"virtual":[137],"sequencing,":[138],"drastically":[139],"reducing":[140],"costs":[141],"while":[142],"integrating":[143],"insights":[145],"pathology":[147],"with":[148],"biomarkers,":[150],"thus":[151],"accelerating":[152],"translation.":[154],"Moreover,":[155],"vision":[157,189],"techniques":[158],"can":[159],"reconstruct":[160],"pixel-aligned":[161],"models,":[164],"overcoming":[165],"technical":[167],"barriers":[168],"acquisition":[171],"advancing":[173],"analytics.":[177],"In":[178],"this":[179],"paper,":[180],"we":[181],"present":[182],"first":[184],"systematic":[185],"survey":[186],"AI":[190],"for":[192],"analytics,":[194],"categorizing":[195],"across":[197],"architectures,":[198],"learning":[199],"paradigms,":[200],"tasks,":[201],"datasets,":[203],"tracing":[205],"their":[206],"technological":[207],"evolution.":[208],"We":[209],"highlight":[210],"challenges":[212],"future":[214],"directions,":[215],"offering":[216],"panoramic":[218],"perspective":[219],"vision-driven":[221,238],"potential":[225],"transform":[227],"both":[228],"basic":[229],"research":[230],"practice.":[233],"The":[234],"curated":[235],"collection":[236],"papers":[240],"available":[242],"at":[243],"https://github.com/hrlblab/computer_vision_spatial_omics.":[244]},"counts_by_year":[],"updated_date":"2026-07-18T07:39:51.176621","created_date":"2026-05-26T00:00:00"}
