{"id":"https://openalex.org/W4226446012","doi":"https://doi.org/10.1117/12.2611957","title":"Dense multi-object 3D glomerular reconstruction and quantification on 2D serial section whole slide images","display_name":"Dense multi-object 3D glomerular reconstruction and quantification on 2D serial section whole slide images","publication_year":2022,"publication_date":"2022-04-04","ids":{"openalex":"https://openalex.org/W4226446012","doi":"https://doi.org/10.1117/12.2611957","pmid":"https://pubmed.ncbi.nlm.nih.gov/37229309"},"language":"en","primary_location":{"id":"doi:10.1117/12.2611957","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2611957","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Medical Imaging 2022: Digital and Computational Pathology","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10208386","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037133367","display_name":"Ruining Deng","orcid":"https://orcid.org/0000-0001-6300-8518"},"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":"Ruining Deng","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","Vanderbilt Univ. (United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt Univ. (United States)","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081514433","display_name":"Haichun Yang","orcid":"https://orcid.org/0000-0003-4265-7492"},"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"]},{"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, Nashville, TN, 37232, USA","Vanderbilt Univ. Medical Ctr. (United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I901861585"]},{"raw_affiliation_string":"Vanderbilt Univ. Medical Ctr. (United States)","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074197453","display_name":"Zuhayr Asad","orcid":"https://orcid.org/0000-0002-2401-5026"},"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":"Zuhayr Asad","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","Vanderbilt Univ. (United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt Univ. (United States)","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029808849","display_name":"Zheyu Zhu","orcid":"https://orcid.org/0000-0001-9980-4137"},"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":"Zheyu Zhu","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","Vanderbilt Univ. (United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt Univ. (United States)","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069768835","display_name":"Shiru Wang","orcid":"https://orcid.org/0000-0003-2438-2341"},"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":"Shiru Wang","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","Vanderbilt Univ. (United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt Univ. (United States)","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016504310","display_name":"Lee Wheless","orcid":"https://orcid.org/0000-0002-8162-5971"},"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"]},{"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":"Lee E. Wheless","raw_affiliation_strings":["Department of Dermatology, Vanderbilt University Medical Center, Nashville TN 37232, USA","Vanderbilt Univ. Medical Ctr. (United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Dermatology, Vanderbilt University Medical Center, Nashville TN 37232, USA","institution_ids":["https://openalex.org/I901861585"]},{"raw_affiliation_string":"Vanderbilt Univ. Medical Ctr. (United States)","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031318134","display_name":"Agnes B. Fogo","orcid":"https://orcid.org/0000-0003-3698-8527"},"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"]},{"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":"Agnes B. Fogo","raw_affiliation_strings":["Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA","Vanderbilt Univ. Medical Ctr. (United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I901861585"]},{"raw_affiliation_string":"Vanderbilt Univ. Medical Ctr. (United States)","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067191302","display_name":"Yuankai Huo","orcid":"https://orcid.org/0000-0002-2096-8065"},"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":"Yuankai Huo","raw_affiliation_strings":["Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","Vanderbilt Univ. (United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Vanderbilt University, Nashville, TN, 37235 USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt Univ. (United States)","institution_ids":["https://openalex.org/I200719446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6938,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.74553058,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"11603","issue":null,"first_page":"17","last_page":"17"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9994999766349792,"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/T10552","display_name":"Colorectal Cancer Screening and Detection","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10052","display_name":"Medical Image Segmentation Techniques","score":0.991599977016449,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8420294523239136},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7154016494750977},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6603670120239258},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6381933689117432},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.6117874979972839},{"id":"https://openalex.org/keywords/kidney-glomerulus","display_name":"Kidney Glomerulus","score":0.495307594537735},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.4743817150592804},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4650973081588745},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4586804211139679},{"id":"https://openalex.org/keywords/volume","display_name":"Volume (thermodynamics)","score":0.4422854781150818},{"id":"https://openalex.org/keywords/kidney","display_name":"Kidney","score":0.10127988457679749},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.09649112820625305},{"id":"https://openalex.org/keywords/glomerulonephritis","display_name":"Glomerulonephritis","score":0.07430195808410645}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8420294523239136},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7154016494750977},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6603670120239258},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6381933689117432},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.6117874979972839},{"id":"https://openalex.org/C2910856063","wikidata":"https://www.wikidata.org/wiki/Q909882","display_name":"Kidney Glomerulus","level":4,"score":0.495307594537735},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.4743817150592804},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4650973081588745},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4586804211139679},{"id":"https://openalex.org/C20556612","wikidata":"https://www.wikidata.org/wiki/Q4469374","display_name":"Volume (thermodynamics)","level":2,"score":0.4422854781150818},{"id":"https://openalex.org/C2780091579","wikidata":"https://www.wikidata.org/wiki/Q9377","display_name":"Kidney","level":2,"score":0.10127988457679749},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.09649112820625305},{"id":"https://openalex.org/C2780368995","wikidata":"https://www.wikidata.org/wiki/Q605006","display_name":"Glomerulonephritis","level":3,"score":0.07430195808410645},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C134018914","wikidata":"https://www.wikidata.org/wiki/Q162606","display_name":"Endocrinology","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1117/12.2611957","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2611957","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Medical Imaging 2022: Digital and Computational Pathology","raw_type":"proceedings-article"},{"id":"pmid:37229309","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37229309","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":"Proceedings of SPIE--the International Society for Optical Engineering","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10208386","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10208386","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc SPIE Int Soc Opt Eng","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:10208386","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10208386","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc SPIE Int Soc Opt Eng","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8","score":0.7099999785423279}],"awards":[{"id":"https://openalex.org/G6718589257","display_name":null,"funder_award_id":"R01 DK056942","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"}],"funders":[{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1521019969","https://openalex.org/W2011445126","https://openalex.org/W2630837129","https://openalex.org/W2921675148","https://openalex.org/W2971487518","https://openalex.org/W3080677331","https://openalex.org/W3090112028","https://openalex.org/W3095093830","https://openalex.org/W3126783352","https://openalex.org/W3130654023","https://openalex.org/W3152250781","https://openalex.org/W4233026140","https://openalex.org/W4295331127","https://openalex.org/W6739696289","https://openalex.org/W6766146636","https://openalex.org/W6770944320","https://openalex.org/W6783985716"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W2156434174","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W2121496884","https://openalex.org/W2387910809","https://openalex.org/W4388446985"],"abstract_inverted_index":{"There":[0],"has":[1],"been":[2],"a":[3,111],"long":[4],"pursuit":[5],"for":[6,75,166],"precise":[7],"and":[8,21,28,36,99,130,139,171],"reproducible":[9],"glomerular":[10,26,73,128,169],"quantification":[11,173],"in":[12,18,46,60,110,137,141],"the":[13,61,120,123,126,147],"field":[14],"of":[15,30,53,103],"renal":[16],"pathology":[17],"both":[19],"research":[20],"clinical":[22],"practice.":[23],"Currently,":[24],"3D":[25,72,80,112,127,168],"identification":[27],"reconstruction":[29,129,170],"large-scale":[31,107],"glomeruli":[32,105],"are":[33,67,119,125],"labor-intensive":[34],"tasks,":[35],"time-consuming":[37],"by":[38],"manual":[39,157],"analysis":[40,56],"on":[41,114],"whole":[42],"slide":[43],"imaging":[44],"(WSI)":[45],"2D":[47,62,175],"serial":[48,54,63,176],"sectioning":[49],"representation.":[50],"The":[51,116,159],"accuracy":[52],"section":[55,177],"is":[57],"also":[58],"limited":[59],"context.":[64],"Moreover,":[65],"there":[66],"no":[68],"approaches":[69],"to":[70],"present":[71],"visualization":[74],"human":[76],"examination":[77],"(volume":[78],"calculation,":[79],"phenotype":[81],"analysis,":[82],"etc.).":[83],"In":[84],"this":[85],"paper,":[86],"we":[87],"introduce":[88],"an":[89,164],"end-to-end":[90,160],"holistic":[91],"deep-learning-based":[92],"method":[93],"that":[94],"achieves":[95,135,151],"automatic":[96],"detection,":[97],"segmentation":[98],"multi-object":[100],"tracking":[101],"(MOT)":[102],"individual":[104],"with":[106,156],"glomerular-registered":[108],"assessment":[109],"context":[113],"WSIs.":[115,178],"high-resolution":[117],"WSIs":[118],"inputs,":[121],"while":[122,146],"outputs":[124],"volume":[131,149,172],"estimation.":[132],"This":[133],"pipeline":[134,162],"81.8":[136],"IDF1":[138],"69.1":[140],"MOTA":[142],"as":[143],"MOT":[144],"performance,":[145],"proposed":[148],"estimation":[150],"0.84":[152],"Spearman":[153],"correlation":[154],"coefficient":[155],"annotation.":[158],"MAP3D+":[161],"provides":[163],"approach":[165],"extensive":[167],"from":[174]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
