{"id":"https://openalex.org/W2994000519","doi":"https://doi.org/10.1093/bioinformatics/btz914","title":"SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells","display_name":"SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells","publication_year":2019,"publication_date":"2019-12-01","ids":{"openalex":"https://openalex.org/W2994000519","doi":"https://doi.org/10.1093/bioinformatics/btz914","mag":"2994000519","pmid":"https://pubmed.ncbi.nlm.nih.gov/31808789"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz914","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz914","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058218566","display_name":"Xiao Tan","orcid":"https://orcid.org/0000-0003-3148-7993"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Xiao Tan","raw_affiliation_strings":["Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, QLD, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090557986","display_name":"Andrew Su","orcid":"https://orcid.org/0000-0003-3638-8628"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Andrew Su","raw_affiliation_strings":["Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, QLD, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101989639","display_name":"Minh Tran","orcid":"https://orcid.org/0000-0003-1088-0243"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Minh Tran","raw_affiliation_strings":["Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, QLD, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034599952","display_name":"Quan Nguyen","orcid":"https://orcid.org/0000-0001-7870-5703"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Quan Nguyen","raw_affiliation_strings":["Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, QLD, Australia"],"raw_orcid":"https://orcid.org/0000-0001-7870-5703","affiliations":[{"raw_affiliation_string":"Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5034599952"],"corresponding_institution_ids":["https://openalex.org/I165143802"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.2057,"has_fulltext":false,"cited_by_count":83,"citation_normalized_percentile":{"value":0.889895,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"36","issue":"7","first_page":"2293","last_page":"2294"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9941999912261963,"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":0.9941999912261963,"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":0.003100000089034438,"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":0.0010999999940395355,"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":0.6537946462631226},{"id":"https://openalex.org/keywords/pixel","display_name":"Pixel","score":0.6327709555625916},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5522034168243408},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4815804958343506},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4765268564224243},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.46443209052085876},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4605163335800171},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4556851387023926},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.44787153601646423},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.44563695788383484},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39718785881996155},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38474124670028687},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.38377076387405396},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.37623587250709534},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.3331904113292694},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26764458417892456},{"id":"https://openalex.org/keywords/remote-sensing","display_name":"Remote sensing","score":0.11467370390892029},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10141029953956604},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.09196138381958008}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6537946462631226},{"id":"https://openalex.org/C160633673","wikidata":"https://www.wikidata.org/wiki/Q355198","display_name":"Pixel","level":2,"score":0.6327709555625916},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5522034168243408},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4815804958343506},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4765268564224243},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.46443209052085876},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4605163335800171},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4556851387023926},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.44787153601646423},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.44563695788383484},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39718785881996155},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38474124670028687},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.38377076387405396},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37623587250709534},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.3331904113292694},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26764458417892456},{"id":"https://openalex.org/C62649853","wikidata":"https://www.wikidata.org/wiki/Q199687","display_name":"Remote sensing","level":1,"score":0.11467370390892029},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10141029953956604},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.09196138381958008},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz914","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz914","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31808789","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31808789","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2604408404","https://openalex.org/W2751723768","https://openalex.org/W2760946358","https://openalex.org/W2808465642","https://openalex.org/W2896334009","https://openalex.org/W2937443931","https://openalex.org/W2952459265","https://openalex.org/W2962001321","https://openalex.org/W2963258365","https://openalex.org/W3100003598","https://openalex.org/W3105973851"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W2942994004","https://openalex.org/W2982720988","https://openalex.org/W3150324899","https://openalex.org/W2523545060","https://openalex.org/W4229998356","https://openalex.org/W4379374180","https://openalex.org/W4388725868"],"abstract_inverted_index":{"MOTIVATION:":[0],"Spatial":[1],"transcriptomics":[2],"(ST)":[3],"technology":[4],"is":[5,125,134],"increasingly":[6],"being":[7],"applied":[8],"because":[9],"it":[10,133],"enables":[11],"the":[12,27,45,85,89],"measurement":[13],"of":[14,26,66,72,91,111],"spatial":[15],"gene":[16,49,73],"expression":[17,50,74],"in":[18,80],"an":[19,129],"intact":[20],"tissue":[21,52,112],"along":[22],"with":[23,70,114],"imaging":[24,96],"morphology":[25],"same":[28],"tissue.":[29,82],"However,":[30],"current":[31],"analysis":[32],"methods":[33],"for":[34],"ST":[35],"data":[36,93,97,141],"do":[37],"not":[38],"use":[39,90],"image":[40],"pixel":[41,67],"information,":[42],"thus":[43],"missing":[44],"quantitative":[46],"links":[47],"between":[48],"and":[51,117,132],"morphology.":[53],"RESULTS:":[54],"We":[55,83],"developed":[56],"a":[57,81],"user-friendly":[58],"deep":[59,101],"learning":[60,102],"software,":[61],"SpaCell,":[62],"to":[63,99,104],"integrate":[64],"millions":[65],"intensity":[68],"values":[69],"thousands":[71],"measurements":[75],"from":[76],"spatially":[77],"barcoded":[78],"spots":[79],"show":[84],"integration":[86],"approach":[87],"outperforms":[88],"gene-count":[92],"alone":[94,98],"or":[95,108],"build":[100],"models":[103],"identify":[105],"cell":[106],"types":[107],"predict":[109],"labels":[110],"images":[113],"high":[115],"resolution":[116],"accuracy.":[118],"AVAILABILITY":[119],"AND":[120],"IMPLEMENTATION:":[121],"The":[122],"SpaCell":[123],"package":[124],"open":[126],"source":[127],"under":[128],"MIT":[130],"licence":[131],"available":[135,143],"at":[136,144],"https://github.com/BiomedicalMachineLearning/SpaCell.":[137],"SUPPLEMENTARY":[138],"INFORMATION:":[139],"Supplementary":[140],"are":[142],"Bioinformatics":[145],"online.":[146]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":4}],"updated_date":"2026-08-08T01:25:22.217667","created_date":"2025-10-10T00:00:00"}