{"id":"https://openalex.org/W4405022772","doi":"https://doi.org/10.1109/jbhi.2024.3511422","title":"3D-Organoid-SwinNet: High-Content Profiling of 3D Organoids","display_name":"3D-Organoid-SwinNet: High-Content Profiling of 3D Organoids","publication_year":2024,"publication_date":"2024-12-04","ids":{"openalex":"https://openalex.org/W4405022772","doi":"https://doi.org/10.1109/jbhi.2024.3511422","pmid":"https://pubmed.ncbi.nlm.nih.gov/40030494"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2024.3511422","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3511422","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11970996/","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045475293","display_name":"Muhammad Sohaib","orcid":"https://orcid.org/0000-0003-0218-3595"},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Muhammad Sohaib","raw_affiliation_strings":["Department Electrical and Biomedical Engineering, University of Nevada, Reno, NV, USA"],"affiliations":[{"raw_affiliation_string":"Department Electrical and Biomedical Engineering, University of Nevada, Reno, NV, USA","institution_ids":["https://openalex.org/I134113660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019743125","display_name":"Siyavash Shabani","orcid":"https://orcid.org/0000-0002-3088-7437"},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Siyavash Shabani","raw_affiliation_strings":["Department Electrical and Biomedical Engineering, University of Nevada, Reno, NV, USA"],"affiliations":[{"raw_affiliation_string":"Department Electrical and Biomedical Engineering, University of Nevada, Reno, NV, USA","institution_ids":["https://openalex.org/I134113660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104336915","display_name":"Sahar A. Mohammed","orcid":null},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sahar A Mohammed","raw_affiliation_strings":["Department Electrical and Biomedical Engineering, University of Nevada, Reno, NV, USA"],"affiliations":[{"raw_affiliation_string":"Department Electrical and Biomedical Engineering, University of Nevada, Reno, NV, USA","institution_ids":["https://openalex.org/I134113660"]}]},{"author_position":"last","author":{"id":null,"display_name":"Bahram Parvin","orcid":"https://orcid.org/0000-0002-6433-8006"},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bahram Parvin","raw_affiliation_strings":["Department Electrical and Biomedical Engineering, University of Nevada, Reno, NV, USA"],"affiliations":[{"raw_affiliation_string":"Department Electrical and Biomedical Engineering, University of Nevada, Reno, NV, USA","institution_ids":["https://openalex.org/I134113660"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5045475293"],"corresponding_institution_ids":["https://openalex.org/I134113660"],"apc_list":null,"apc_paid":null,"fwci":1.0215,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.78682762,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"29","issue":"2","first_page":"792","last_page":"798"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10036","display_name":"Advanced Neural Network Applications","score":0.9878000020980835,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10036","display_name":"Advanced Neural Network Applications","score":0.9878000020980835,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9595000147819519,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11190","display_name":"3D Printing in Biomedical Research","score":0.9585000276565552,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/organoid","display_name":"Organoid","score":0.9684791564941406},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.5788492560386658},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5119684934616089},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16643866896629333},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.14710134267807007},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12411963939666748}],"concepts":[{"id":"https://openalex.org/C31695470","wikidata":"https://www.wikidata.org/wiki/Q11293125","display_name":"Organoid","level":2,"score":0.9684791564941406},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5788492560386658},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5119684934616089},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16643866896629333},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.14710134267807007},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12411963939666748}],"mesh":[{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D009940","descriptor_name":"Organoids","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D009940","descriptor_name":"Organoids","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D009940","descriptor_name":"Organoids","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D009940","descriptor_name":"Organoids","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D009940","descriptor_name":"Organoids","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D009940","descriptor_name":"Organoids","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D009940","descriptor_name":"Organoids","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1109/jbhi.2024.3511422","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3511422","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:40030494","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40030494","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":"IEEE journal of biomedical and health informatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11690809","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11970996","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:11970996","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11970996/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE J Biomed Health Inform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:11970996","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11970996/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE J Biomed Health Inform","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1901129140","https://openalex.org/W1967293289","https://openalex.org/W1980324695","https://openalex.org/W2054922344","https://openalex.org/W2127362646","https://openalex.org/W2146017443","https://openalex.org/W2307244832","https://openalex.org/W2464708700","https://openalex.org/W2620591646","https://openalex.org/W2826154191","https://openalex.org/W2883890990","https://openalex.org/W2962914239","https://openalex.org/W2989380501","https://openalex.org/W2999770235","https://openalex.org/W3012399185","https://openalex.org/W3035084800","https://openalex.org/W3132542462","https://openalex.org/W3183708017","https://openalex.org/W3211490618","https://openalex.org/W4200561569","https://openalex.org/W4206337522","https://openalex.org/W4220813465","https://openalex.org/W4221163766","https://openalex.org/W4286111664","https://openalex.org/W4308624890","https://openalex.org/W4311481072","https://openalex.org/W4390874575","https://openalex.org/W6784333009","https://openalex.org/W6797399245"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4386439204","https://openalex.org/W4401794395","https://openalex.org/W3133804457","https://openalex.org/W3033121461","https://openalex.org/W3094248195","https://openalex.org/W2811397904","https://openalex.org/W3047600752"],"abstract_inverted_index":{"Profiling":[0],"of":[1,17,82,110,116,138],"Patient-Derived":[2],"organoids":[3],"is":[4],"necessary":[5,43],"for":[6,44,74,131,135],"drug":[7],"screening":[8],"and":[9,60,103],"precision":[10],"medicine.":[11],"This":[12],"step":[13],"requires":[14],"accurate":[15,45],"segmentation":[16,70],"three-dimensional":[18],"cellular":[19],"structures":[20],"followed":[21],"by":[22,63],"protein":[23],"readouts.":[24],"While":[25],"fully":[26],"Convolutional":[27],"Neural":[28],"Networks":[29],"are":[30],"widely":[31],"used":[32],"in":[33,56,99],"medical":[34],"image":[35],"segmentation,":[36],"they":[37],"struggle":[38],"to":[39,118],"capture":[40],"long-range":[41,58],"dependencies":[42,59],"segmentation.":[46,77],"On":[47],"the":[48,80,101,114,125],"other":[49],"hand,":[50],"transformer":[51],"models":[52,133],"have":[53],"shown":[54],"promise":[55],"capturing":[57],"self-similarities.":[61],"Motivated":[62],"this,":[64],"we":[65],"present":[66],"3D-Organoid-SwinNet,":[67],"a":[68,107,129],"unique":[69],"model":[71,127],"explicitly":[72],"designed":[73,134],"organoid":[75,139],"semantic":[76],"We":[78,94],"evaluated":[79],"performance":[81,98],"our":[83],"technique":[84],"using":[85],"an":[86],"Organoid":[87],"dataset":[88],"from":[89],"four":[90],"breast":[91],"cancer":[92],"subtypes.":[93],"demonstrated":[95],"consistent":[96],"top-tier":[97],"both":[100],"validation":[102],"testing":[104],"phases,":[105],"achieving":[106],"Dice":[108],"score":[109],"94.91":[111],"while":[112],"reducing":[113],"number":[115],"parameters":[117],"21":[119],"million.":[120],"Our":[121],"findings":[122],"indicate":[123],"that":[124],"proposed":[126],"offers":[128],"foundation":[130],"transformer-based":[132],"high-content":[136],"profiling":[137],"models.":[140]},"counts_by_year":[{"year":2025,"cited_by_count":4}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
