{"id":"https://openalex.org/W3130651713","doi":"https://doi.org/10.1117/12.2581060","title":"Managing class imbalance of immune cell populations in multi-class instance segmentation of immunofluorescence images of Lupus Nephritis biopsies","display_name":"Managing class imbalance of immune cell populations in multi-class instance segmentation of immunofluorescence images of Lupus Nephritis biopsies","publication_year":2021,"publication_date":"2021-02-12","ids":{"openalex":"https://openalex.org/W3130651713","doi":"https://doi.org/10.1117/12.2581060","mag":"3130651713"},"language":"en","primary_location":{"id":"doi:10.1117/12.2581060","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2581060","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Medical Imaging 2021: Digital Pathology","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5038128771","display_name":"Madeleine S. Durkee","orcid":"https://orcid.org/0000-0003-0543-074X"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Madeleine S. Durkee","raw_affiliation_strings":["The Univ. of Chicago (United States)"],"affiliations":[{"raw_affiliation_string":"The Univ. of Chicago (United States)","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079139261","display_name":"Rebecca Abraham","orcid":"https://orcid.org/0000-0001-8422-8675"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rebecca Abraham","raw_affiliation_strings":["The Univ. of Chicago (United States)"],"affiliations":[{"raw_affiliation_string":"The Univ. of Chicago (United States)","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078316765","display_name":"Junting Ai","orcid":null},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junting Ai","raw_affiliation_strings":["The Univ. of Chicago (United States)"],"affiliations":[{"raw_affiliation_string":"The Univ. of Chicago (United States)","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027395645","display_name":"Marcus R. Clark","orcid":"https://orcid.org/0000-0003-4747-0387"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marcus R. Clark","raw_affiliation_strings":["The Univ. of Chicago (United States)"],"affiliations":[{"raw_affiliation_string":"The Univ. of Chicago (United States)","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049042648","display_name":"Maryellen L. Giger","orcid":"https://orcid.org/0000-0001-5482-9728"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maryellen L. Giger","raw_affiliation_strings":["The Univ. of Chicago (United States)"],"affiliations":[{"raw_affiliation_string":"The Univ. of Chicago (United States)","institution_ids":["https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5038128771"],"corresponding_institution_ids":["https://openalex.org/I40347166"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.02228524,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"36","last_page":"36"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10308","display_name":"Systemic Lupus Erythematosus Research","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10308","display_name":"Systemic Lupus Erythematosus Research","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9955000281333923,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10981","display_name":"Cytomegalovirus and herpesvirus research","score":0.987500011920929,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.6179391741752625},{"id":"https://openalex.org/keywords/lupus-nephritis","display_name":"Lupus nephritis","score":0.6076295375823975},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5353700518608093},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.45567238330841064},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.445843368768692},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.43446409702301025},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40876275300979614},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3932930827140808},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2911689877510071},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.28236716985702515},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.2537056803703308},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.14930087327957153}],"concepts":[{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.6179391741752625},{"id":"https://openalex.org/C2779912601","wikidata":"https://www.wikidata.org/wiki/Q1621830","display_name":"Lupus nephritis","level":3,"score":0.6076295375823975},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5353700518608093},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.45567238330841064},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.445843368768692},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.43446409702301025},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40876275300979614},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3932930827140808},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2911689877510071},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.28236716985702515},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.2537056803703308},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.14930087327957153}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1117/12.2581060","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2581060","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Medical Imaging 2021: Digital Pathology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4225547319","https://openalex.org/W4311533834","https://openalex.org/W2077866618","https://openalex.org/W2471395144","https://openalex.org/W4380993043","https://openalex.org/W2364717911","https://openalex.org/W2513259431","https://openalex.org/W1973618035","https://openalex.org/W2391027603","https://openalex.org/W1975062275"],"abstract_inverted_index":{"Lupus":[0],"nephritis":[1],"(LuN)":[2],"is":[3,28,98],"a":[4,46,81],"manifestation":[5],"of":[6,14,48,53,128,208,217,229],"systemic":[7],"lupus":[8],"erythematosus":[9],"defined":[10],"by":[11,100],"chronic":[12],"infiltration":[13],"immune":[15,231],"cells":[16,23],"into":[17],"the":[18,31,150,186,230],"kidneys\u2014particularly":[19],"lymphocytes":[20,106,132],"and":[21,69,107,131],"dendritic":[22],"(DCs).":[24],"Ultimately,":[25],"our":[26],"goal":[27],"to":[29,37,85,123,139,147,155,175,213,222],"characterize":[30],"cellular":[32],"communities":[33],"associated":[34],"with":[35,80,109,158,177,204],"progression":[36],"kidney":[38,54],"failure.":[39],"To":[40],"accomplish":[41],"this,":[42],"we":[43,116],"have":[44,61],"generated":[45],"dataset":[47],"fluorescence":[49],"confocal":[50],"microscopy":[51],"images":[52,157],"biopsies":[55],"from":[56,173,202,211],"31":[57],"LuN":[58,134,223,239],"patients":[59],"that":[60,233],"been":[62],"stained":[63],"for":[64,119,191],"two":[65,70],"T-lymphocyte":[66],"populations,":[67],"B-lymphocytes":[68],"DC":[71,165,181,192,195],"populations.":[72],"We":[73],"are":[74],"using":[75],"convolutional":[76],"neural":[77],"networks":[78],"(CNNs)":[79],"Mask":[82],"R-CNN":[83],"architecture":[84],"perform":[86],"instance":[87,95,126],"segmentation":[88,96,127,182,216],"on":[89,167],"these":[90],"five":[91],"classes.":[92,193],"This":[93],"multi-class":[94],"task":[97],"hindered":[99],"an":[101,168],"inherent":[102],"class":[103,121],"imbalance":[104,122],"between":[105],"DCs,":[108],"DCs":[110,130,148,209],"being":[111],"much":[112],"less":[113],"prevalent.":[114],"Here":[115],"discuss":[117],"methods":[118],"managing":[120],"achieve":[124],"comparable":[125],"both":[129],"in":[133,235,238],"biopsies.":[135],"A":[136],"network":[137,187],"trained":[138,189,200],"identify":[140],"all":[141,159,218],"5":[142,160],"classes":[143,162],"yielded":[144],"higher":[145],"sensitivity":[146,166,196],"when":[149,185,199],"training":[151,179],"set":[152,171],"was":[153,188],"filtered":[154,178],"contain":[156],"cell":[161,219],"present.":[163],"Average":[164,194],"independent":[169],"test":[170],"improved":[172,183],"0.54":[174],"0.63":[176],"data.":[180],"further":[184],"specifically":[190],"reached":[197],"0.91":[198],"separately":[201],"lymphocytes,":[203],"average":[205],"Jaccard":[206],"index":[207],"improving":[210],"0.69\u00b10.2":[212],"0.76\u00b10.2.":[214],"Accurate":[215],"types":[220],"relevant":[221],"pathogenesis":[224],"enabled":[225],"in-depth":[226],"spatial":[227],"analysis":[228],"environments":[232],"result":[234],"renal":[236],"failure":[237],"patients.":[240]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}