{"id":"https://openalex.org/W4403145699","doi":"https://doi.org/10.1093/bib/bbae476","title":"An initial game-theoretic assessment of enhanced tissue preparation and imaging protocols for improved deep learning inference of spatial transcriptomics from tissue morphology","display_name":"An initial game-theoretic assessment of enhanced tissue preparation and imaging protocols for improved deep learning inference of spatial transcriptomics from tissue morphology","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4403145699","doi":"https://doi.org/10.1093/bib/bbae476","pmid":"https://pubmed.ncbi.nlm.nih.gov/39367648"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae476","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae476","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae476/59580854/bbae476.pdf","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://academic.oup.com/bib/article-pdf/25/6/bbae476/59580854/bbae476.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036608392","display_name":"Michael Fatemi","orcid":null},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael Y Fatemi","raw_affiliation_strings":["Department of Computer Science, University of Virginia , Charlottesville, VA 22903,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Virginia , Charlottesville, VA 22903,","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017439671","display_name":"Yunrui Lu","orcid":"https://orcid.org/0000-0003-1089-9323"},"institutions":[{"id":"https://openalex.org/I4390039337","display_name":"Dartmouth Health","ror":"https://ror.org/01pa9ed26","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I107672454","https://openalex.org/I4390039337"]}],"countries":["LB"],"is_corresponding":false,"raw_author_name":"Yunrui Lu","raw_affiliation_strings":["Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":["https://openalex.org/I4390039337"]},{"raw_affiliation_string":"Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022033375","display_name":"Alos Diallo","orcid":"https://orcid.org/0000-0002-6471-4630"},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]},{"id":"https://openalex.org/I4390039337","display_name":"Dartmouth Health","ror":"https://ror.org/01pa9ed26","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I107672454","https://openalex.org/I4390039337"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alos B Diallo","raw_affiliation_strings":["Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","Department of Epidemiology, Dartmouth College Geisel School of Medicine , Hanover, NH 03756,","Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","Program in Quantitative Biomedical Sciences, Dartmouth College Geisel School of Medicine , Hanover, NH 03756,"],"raw_orcid":"https://orcid.org/0000-0002-6471-4630","affiliations":[{"raw_affiliation_string":"Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":["https://openalex.org/I4390039337"]},{"raw_affiliation_string":"Department of Epidemiology, Dartmouth College Geisel School of Medicine , Hanover, NH 03756,","institution_ids":["https://openalex.org/I107672454"]},{"raw_affiliation_string":"Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":[]},{"raw_affiliation_string":"Program in Quantitative Biomedical Sciences, Dartmouth College Geisel School of Medicine , Hanover, NH 03756,","institution_ids":["https://openalex.org/I107672454"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072382821","display_name":"Gokul Raghavendra Srinivasan","orcid":"https://orcid.org/0000-0002-9836-4851"},"institutions":[{"id":"https://openalex.org/I4390039337","display_name":"Dartmouth Health","ror":"https://ror.org/01pa9ed26","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I107672454","https://openalex.org/I4390039337"]}],"countries":["LB"],"is_corresponding":false,"raw_author_name":"Gokul Srinivasan","raw_affiliation_strings":["Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":["https://openalex.org/I4390039337"]},{"raw_affiliation_string":"Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073926694","display_name":"Zarif Azher","orcid":"https://orcid.org/0000-0003-1604-692X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zarif L Azher","raw_affiliation_strings":["Thomas Jefferson High School for Science and Technology , Alexandria, VA 22312,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Thomas Jefferson High School for Science and Technology , Alexandria, VA 22312,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081393377","display_name":"Brock C. Christensen","orcid":"https://orcid.org/0000-0003-3022-426X"},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brock C Christensen","raw_affiliation_strings":["Department of Epidemiology, Dartmouth College Geisel School of Medicine , Hanover, NH 03756,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology, Dartmouth College Geisel School of Medicine , Hanover, NH 03756,","institution_ids":["https://openalex.org/I107672454"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082545896","display_name":"Lucas A. Salas","orcid":"https://orcid.org/0000-0002-2279-4097"},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lucas A Salas","raw_affiliation_strings":["Department of Epidemiology, Dartmouth College Geisel School of Medicine , Hanover, NH 03756,"],"raw_orcid":"https://orcid.org/0000-0002-2279-4097","affiliations":[{"raw_affiliation_string":"Department of Epidemiology, Dartmouth College Geisel School of Medicine , Hanover, NH 03756,","institution_ids":["https://openalex.org/I107672454"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107929170","display_name":"Gregory J. Tsongalis","orcid":null},"institutions":[{"id":"https://openalex.org/I4390039337","display_name":"Dartmouth Health","ror":"https://ror.org/01pa9ed26","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I107672454","https://openalex.org/I4390039337"]}],"countries":["LB"],"is_corresponding":false,"raw_author_name":"Gregory J Tsongalis","raw_affiliation_strings":["Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":["https://openalex.org/I4390039337"]},{"raw_affiliation_string":"Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013283010","display_name":"Scott Palisoul","orcid":null},"institutions":[{"id":"https://openalex.org/I4390039337","display_name":"Dartmouth Health","ror":"https://ror.org/01pa9ed26","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I107672454","https://openalex.org/I4390039337"]}],"countries":["LB"],"is_corresponding":false,"raw_author_name":"Scott M Palisoul","raw_affiliation_strings":["Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":["https://openalex.org/I4390039337"]},{"raw_affiliation_string":"Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083964091","display_name":"Laurent Perreard","orcid":null},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]},{"id":"https://openalex.org/I4390039367","display_name":"Dartmouth Cancer Center","ror":"https://ror.org/044b05b34","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4390039367"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laurent Perreard","raw_affiliation_strings":["Genomics Shared Resource, Dartmouth Cancer Center , Lebanon, NH 03756,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomics Shared Resource, Dartmouth Cancer Center , Lebanon, NH 03756,","institution_ids":["https://openalex.org/I107672454","https://openalex.org/I4390039367"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065035721","display_name":"Fred Kolling","orcid":"https://orcid.org/0000-0002-6178-9901"},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]},{"id":"https://openalex.org/I4390039367","display_name":"Dartmouth Cancer Center","ror":"https://ror.org/044b05b34","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4390039367"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fred W Kolling","raw_affiliation_strings":["Genomics Shared Resource, Dartmouth Cancer Center , Lebanon, NH 03756,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomics Shared Resource, Dartmouth Cancer Center , Lebanon, NH 03756,","institution_ids":["https://openalex.org/I107672454","https://openalex.org/I4390039367"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075327685","display_name":"Louis Vaickus","orcid":"https://orcid.org/0000-0002-8989-9539"},"institutions":[{"id":"https://openalex.org/I4390039337","display_name":"Dartmouth Health","ror":"https://ror.org/01pa9ed26","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I107672454","https://openalex.org/I4390039337"]}],"countries":["LB"],"is_corresponding":false,"raw_author_name":"Louis J Vaickus","raw_affiliation_strings":["Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":["https://openalex.org/I4390039337"]},{"raw_affiliation_string":"Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053202754","display_name":"Joshua Levy","orcid":"https://orcid.org/0000-0001-8050-1291"},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]},{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]},{"id":"https://openalex.org/I4390039337","display_name":"Dartmouth Health","ror":"https://ror.org/01pa9ed26","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I107672454","https://openalex.org/I4390039337"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua J Levy","raw_affiliation_strings":["Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","Department of Computational Biomedicine, Cedars Sinai Medical Center , Los Angeles, CA 90048,","Department of Dermatology, Dartmouth Health , Lebanon, NH 03756,","Department of Epidemiology, Dartmouth College Geisel School of Medicine , Hanover, NH 03756,","Department of Pathology and Laboratory Medicine, Cedars Sinai Medical Center , Los Angeles, CA 90048,","Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","Program in Quantitative Biomedical Sciences, Dartmouth College Geisel School of Medicine , Hanover, NH 03756,"],"raw_orcid":"https://orcid.org/0000-0001-8050-1291","affiliations":[{"raw_affiliation_string":"Dartmouth Health , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":["https://openalex.org/I4390039337"]},{"raw_affiliation_string":"Department of Computational Biomedicine, Cedars Sinai Medical Center , Los Angeles, CA 90048,","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Department of Dermatology, Dartmouth Health , Lebanon, NH 03756,","institution_ids":["https://openalex.org/I4390039337"]},{"raw_affiliation_string":"Department of Epidemiology, Dartmouth College Geisel School of Medicine , Hanover, NH 03756,","institution_ids":["https://openalex.org/I107672454"]},{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, Cedars Sinai Medical Center , Los Angeles, CA 90048,","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Emerging Diagnostic and Investigative Technologies , Department of Pathology and Laboratory Medicine, , Lebanon, NH 03766,","institution_ids":[]},{"raw_affiliation_string":"Program in Quantitative Biomedical Sciences, Dartmouth College Geisel School of Medicine , Hanover, NH 03756,","institution_ids":["https://openalex.org/I107672454"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5036608392"],"corresponding_institution_ids":["https://openalex.org/I51556381"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.6867,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.84313618,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"25","issue":"6","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":0.9995999932289124,"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":0.9995999932289124,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9872999787330627,"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":0.9804999828338623,"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/computer-science","display_name":"Computer science","score":0.6574292778968811},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.6367718577384949},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6364848613739014},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6073780059814453},{"id":"https://openalex.org/keywords/h-e-stain","display_name":"H&E stain","score":0.5229721069335938},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4293064773082733},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.38961073756217957},{"id":"https://openalex.org/keywords/biomedical-engineering","display_name":"Biomedical engineering","score":0.35347965359687805},{"id":"https://openalex.org/keywords/staining","display_name":"Staining","score":0.33944860100746155},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2266966998577118}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6574292778968811},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6367718577384949},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6364848613739014},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6073780059814453},{"id":"https://openalex.org/C125473707","wikidata":"https://www.wikidata.org/wiki/Q9914","display_name":"H&E stain","level":3,"score":0.5229721069335938},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4293064773082733},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.38961073756217957},{"id":"https://openalex.org/C136229726","wikidata":"https://www.wikidata.org/wiki/Q327092","display_name":"Biomedical engineering","level":1,"score":0.35347965359687805},{"id":"https://openalex.org/C74864618","wikidata":"https://www.wikidata.org/wiki/Q2332446","display_name":"Staining","level":2,"score":0.33944860100746155},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2266966998577118}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005716","descriptor_name":"Game Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005716","descriptor_name":"Game Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005716","descriptor_name":"Game Theory","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":"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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D014024","descriptor_name":"Tissues","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D014024","descriptor_name":"Tissues","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D014024","descriptor_name":"Tissues","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D014024","descriptor_name":"Tissues","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D014024","descriptor_name":"Tissues","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D014024","descriptor_name":"Tissues","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"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":false},{"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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D056808","descriptor_name":"Biostatistics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056808","descriptor_name":"Biostatistics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056808","descriptor_name":"Biostatistics","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"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/bbae476","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae476","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae476/59580854/bbae476.pdf","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:39367648","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39367648","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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11452536","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11452536","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11452536/pdf/bbae476.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,"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/bbae476","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae476","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae476/59580854/bbae476.pdf","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":[],"awards":[{"id":"https://openalex.org/G1870629651","display_name":null,"funder_award_id":"5P30CA023108","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3521523268","display_name":null,"funder_award_id":"1S10OD030242","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3681109530","display_name":null,"funder_award_id":"P20GM104416","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3831149079","display_name":null,"funder_award_id":"P20GM104416","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6498549891","display_name":null,"funder_award_id":"P20GM130454","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7704875341","display_name":null,"funder_award_id":"P20GM130454","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8062215747","display_name":null,"funder_award_id":"P20GM104416","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G8569647026","display_name":null,"funder_award_id":"5P30CA023108","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8754140588","display_name":null,"funder_award_id":"S10OD025235","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320310400","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"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/W4403145699.pdf","grobid_xml":"https://content.openalex.org/works/W4403145699.grobid-xml"},"referenced_works_count":78,"referenced_works":["https://openalex.org/W1825242443","https://openalex.org/W1997845311","https://openalex.org/W2007296198","https://openalex.org/W2022058776","https://openalex.org/W2034191733","https://openalex.org/W2038766282","https://openalex.org/W2065857975","https://openalex.org/W2070050178","https://openalex.org/W2109374370","https://openalex.org/W2117753404","https://openalex.org/W2132162500","https://openalex.org/W2162445773","https://openalex.org/W2801309958","https://openalex.org/W2807701194","https://openalex.org/W2883217373","https://openalex.org/W2885079199","https://openalex.org/W2889326414","https://openalex.org/W2945212106","https://openalex.org/W2949574275","https://openalex.org/W2953036966","https://openalex.org/W2982390575","https://openalex.org/W3013528572","https://openalex.org/W3014247824","https://openalex.org/W3022836409","https://openalex.org/W3036882247","https://openalex.org/W3043614220","https://openalex.org/W3043793790","https://openalex.org/W3046305306","https://openalex.org/W3047106569","https://openalex.org/W3091885231","https://openalex.org/W3092703718","https://openalex.org/W3096881394","https://openalex.org/W3098491829","https://openalex.org/W3109657403","https://openalex.org/W3111565185","https://openalex.org/W3118539370","https://openalex.org/W3134482219","https://openalex.org/W3154820754","https://openalex.org/W3158391114","https://openalex.org/W3165120573","https://openalex.org/W3165827221","https://openalex.org/W3186679119","https://openalex.org/W3190202966","https://openalex.org/W3208940117","https://openalex.org/W4220765701","https://openalex.org/W4220897949","https://openalex.org/W4223436014","https://openalex.org/W4229007625","https://openalex.org/W4237903802","https://openalex.org/W4285803722","https://openalex.org/W4285822031","https://openalex.org/W4308375572","https://openalex.org/W4308378253","https://openalex.org/W4320719442","https://openalex.org/W4323320361","https://openalex.org/W4328048773","https://openalex.org/W4361290675","https://openalex.org/W4362542941","https://openalex.org/W4376132106","https://openalex.org/W4382447931","https://openalex.org/W4382918425","https://openalex.org/W4383621593","https://openalex.org/W4383744963","https://openalex.org/W4383896402","https://openalex.org/W4384830693","https://openalex.org/W4385410075","https://openalex.org/W4385454187","https://openalex.org/W4386031249","https://openalex.org/W4386946660","https://openalex.org/W4387499879","https://openalex.org/W4390242455","https://openalex.org/W4390500930","https://openalex.org/W4390542364","https://openalex.org/W6679648742","https://openalex.org/W6760064560","https://openalex.org/W6762234667","https://openalex.org/W6854710267","https://openalex.org/W6855016108"],"related_works":["https://openalex.org/W2383463315","https://openalex.org/W3163749585","https://openalex.org/W4399790878","https://openalex.org/W3080438050","https://openalex.org/W4394857391","https://openalex.org/W4394840445","https://openalex.org/W2063962692","https://openalex.org/W2044206368","https://openalex.org/W2392756543","https://openalex.org/W3216304216"],"abstract_inverted_index":{"The":[0,252],"application":[1],"of":[2,69,186,201,214,278,311,315,326,369],"deep":[3,76,159,316],"learning":[4,77,317],"to":[5,35,172,195,257,269,296,359,365],"spatial":[6,32,47,81,279,351],"transcriptomics":[7],"(ST)":[8],"can":[9,29,74,144,348],"reveal":[10],"relationships":[11],"between":[12],"gene":[13,24,237],"expression":[14,25,238],"and":[15,72,85,126,140,153,176,184,227,259,285,329],"tissue":[16,27,70,124,138,189,242],"architecture.":[17],"Prior":[18,92],"work":[19],"has":[20],"demonstrated":[21],"that":[22,122,129,283,345],"inferring":[23],"from":[26,83,97,163,249,354],"histomorphology":[28],"discern":[30],"these":[31],"molecular":[33],"markers":[34,371],"enable":[36],"population":[37],"scale":[38],"studies,":[39],"reducing":[40],"the":[41,67,168,212,271,275,291,297,309,313,321,324,342,367],"fiscal":[42,306],"barriers":[43],"associated":[44],"with":[45,105],"large-scale":[46],"profiling.":[48,197,280],"However,":[49],"while":[50],"most":[51],"improvements":[52],"in":[53,301],"algorithmic":[54],"performance":[55,213,262,303],"have":[56,349],"focused":[57],"on":[58,107,114,217,264,287,350],"improving":[59],"model":[60,78,147],"architectures,":[61],"little":[62],"is":[63,117,331,357],"known":[64],"about":[65],"how":[66],"quality":[68],"preparation":[71],"imaging":[73,106,127,154,330],"affect":[75],"training":[79,284],"for":[80,88,94,132,158],"inference":[82,96,162,353],"morphology":[84],"its":[86],"potential":[87],"widespread":[89],"clinical":[90,133,141],"adoption.":[91],"studies":[93],"ST":[95,115,161,196],"histology":[98],"typically":[99],"utilize":[100],"manually":[101],"stained":[102],"frozen":[103],"sections":[104,190,243],"non-clinical":[108],"grade":[109,142],"scanners.":[110],"Training":[111],"such":[112,361],"models":[113,215],"cohorts":[116],"also":[118],"costly.":[119],"We":[120],"hypothesize":[121],"adopting":[123],"processing":[125,152,328,363],"practices":[128],"mirror":[130],"standards":[131],"implementation":[134],"(permanent":[135],"sections,":[136],"automated":[137,174],"staining,":[139],"scanning)":[143],"significantly":[145],"improve":[146],"performance.":[148],"An":[149],"enhanced":[150,221,272,292],"specimen":[151,327,346],"protocol":[155,166,273,293],"was":[156,255],"developed":[157],"learning-based":[160],"morphology.":[164,355],"This":[165,334],"featured":[167],"Visium":[169],"CytAssist":[170],"assay":[171],"permit":[173],"hematoxylin":[175],"eosin":[177],"staining":[178,226],"(e.g.":[179],"Leica":[180],"Bond),":[181],"40\u00d7-resolution":[182],"imaging,":[183],"joining":[185],"multiple":[187],"patients'":[188],"per":[191],"capture":[192],"area":[193],"prior":[194],"Using":[198],"a":[199,265,338,373],"cohort":[200],"13":[202],"pathologic":[203],"T":[204],"Stage-III":[205],"stage":[206],"colorectal":[207],"cancer":[208],"patients,":[209],"we":[210,235],"compared":[211],"trained":[216],"slide":[218,246],"prepared":[219],"using":[220,244,270],"versus":[222,274],"traditional":[223,298],"(i.e.":[224],"manual":[225],"low-resolution":[228],"imaging)":[229],"protocols.":[230,251],"Leveraging":[231],"Inceptionv3":[232],"neural":[233],"networks,":[234],"predicted":[236],"across":[239],"serial,":[240],"histologically-matched":[241],"whole":[245],"images":[247],"(WSI)":[248],"both":[250],"data":[253],"Shapley":[254],"used":[256],"quantify":[258],"compare":[260],"marginal":[261],"gains":[263],"patient-by-patient":[266],"basis":[267],"attributed":[268],"actual":[276],"costs":[277],"Findings":[281],"indicate":[282],"validating":[286],"WSI":[288],"acquired":[289],"through":[290,337],"as":[294],"opposed":[295],"method":[299],"resulted":[300],"improved":[302],"at":[304,372],"lower":[305],"cost.":[307],"In":[308],"realm":[310],"ST,":[312],"enhancement":[314],"architectures":[318],"frequently":[319],"captures":[320],"spotlight;":[322],"however,":[323],"significance":[325],"often":[332],"understated.":[333],"research,":[335],"informed":[336],"game-theoretic":[339],"lens,":[340],"underscores":[341],"substantial":[343],"impact":[344],"preparation/imaging":[347],"transcriptomic":[352],"It":[356],"essential":[358],"integrate":[360],"optimized":[362],"protocols":[364],"facilitate":[366],"identification":[368],"prognostic":[370],"larger":[374],"scale.":[375]},"counts_by_year":[{"year":2025,"cited_by_count":8}],"updated_date":"2026-05-24T08:33:08.758527","created_date":"2025-10-10T00:00:00"}
