{"id":"https://openalex.org/W3010866839","doi":"https://doi.org/10.1117/12.2549751","title":"Improved instance segmentation of immune cells in human lupus nephritis biopsies with Mask R-CNN","display_name":"Improved instance segmentation of immune cells in human lupus nephritis biopsies with Mask R-CNN","publication_year":2020,"publication_date":"2020-03-16","ids":{"openalex":"https://openalex.org/W3010866839","doi":"https://doi.org/10.1117/12.2549751","mag":"3010866839"},"language":"en","primary_location":{"id":"doi:10.1117/12.2549751","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2549751","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Medical Imaging 2020: 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/A5085108911","display_name":"Adam Sibley","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":"Adam Sibley","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/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/A5077742151","display_name":"Vladimir M. Liarski","orcid":"https://orcid.org/0000-0001-7533-0491"},"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":"Vladimir M. Liarski","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":7,"corresponding_author_ids":["https://openalex.org/A5038128771"],"corresponding_institution_ids":["https://openalex.org/I40347166"],"apc_list":null,"apc_paid":null,"fwci":0.6998,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.69866595,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"46","last_page":"46"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10308","display_name":"Systemic Lupus Erythematosus Research","score":0.995199978351593,"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":0.995199978351593,"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/T13114","display_name":"Image Processing Techniques and Applications","score":0.9581999778747559,"subfield":{"id":"https://openalex.org/subfields/2214","display_name":"Media Technology"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12015","display_name":"Photoacoustic and Ultrasonic Imaging","score":0.9480999708175659,"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/lupus-nephritis","display_name":"Lupus nephritis","score":0.8081940412521362},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.6160632371902466},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.6030045747756958},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5769691467285156},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5660056471824646},{"id":"https://openalex.org/keywords/systemic-lupus-erythematosus","display_name":"Systemic lupus erythematosus","score":0.45075154304504395},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4212944209575653},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.3686884641647339},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3339746594429016},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.31429511308670044},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.2580561935901642},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19907847046852112},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.0765017569065094}],"concepts":[{"id":"https://openalex.org/C2779912601","wikidata":"https://www.wikidata.org/wiki/Q1621830","display_name":"Lupus nephritis","level":3,"score":0.8081940412521362},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.6160632371902466},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.6030045747756958},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5769691467285156},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5660056471824646},{"id":"https://openalex.org/C2776912625","wikidata":"https://www.wikidata.org/wiki/Q1485","display_name":"Systemic lupus erythematosus","level":3,"score":0.45075154304504395},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4212944209575653},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3686884641647339},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3339746594429016},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.31429511308670044},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.2580561935901642},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19907847046852112},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0765017569065094}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1117/12.2549751","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2549751","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Medical Imaging 2020: 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/W2471395144","https://openalex.org/W2098134050","https://openalex.org/W2776803289","https://openalex.org/W2778847013","https://openalex.org/W2364717911","https://openalex.org/W2158944380","https://openalex.org/W3166910253","https://openalex.org/W2951958669","https://openalex.org/W3214891379","https://openalex.org/W2177092523"],"abstract_inverted_index":{"We":[0,57],"demonstrate":[1],"an":[2],"instance":[3,230],"segmentation":[4,168,231],"method":[5,228],"with":[6,88,145,154],"Mask":[7,60,99,164,222],"R-CNN":[8,61,100,165,223],"using":[9],"a":[10,47,226],"ResNet-101":[11],"plus":[12],"Feature":[13],"Pyramid":[14],"Network":[15],"convolutional":[16,51],"backbone":[17],"to":[18,110,116,132,158,181,186,194,207,210],"segment":[19],"and":[20,24,75,92,122,150,169,188],"classify":[21],"T":[22,97,147],"cells":[23,27,91,234],"antigen":[25],"presenting":[26],"(APCs)":[28],"in":[29,140,205,235,244],"multi-channel":[30],"fluorescence":[31,67],"confocal":[32,68],"images.":[33],"This":[34],"network":[35,53],"improves":[36],"on":[37,62],"our":[38],"previous":[39],"cell":[40,55,106,120,148,174,212],"distance":[41],"mapping":[42],"(CDM)":[43],"pipeline,":[44],"which":[45],"used":[46],"custom":[48],"10-":[49],"layer":[50],"neural":[52],"for":[54,214,229,238],"segmentation.":[56],"have":[58],"validated":[59],"two":[63,93,146,151],"independent":[64],"datasets":[65],"of":[66,95,162,216,219,232,241],"images:":[69],"1)":[70],"mouse":[71],"lymph":[72],"node":[73],"tissue,":[74],"2)":[76],"human":[77],"lupus":[78],"nephritis":[79],"(LuN)":[80],"biopsies.":[81],"For":[82],"dataset":[83,141],"1,":[84],"mice":[85],"were":[86,143],"injected":[87],"fluorescent":[89,96],"dendritic":[90],"populations":[94,161],"cells.":[98,221],"improved":[101,113,128,167],"sensitivity":[102,178],"averaged":[103,171],"across":[104,118,172],"all":[105,119,173],"types":[107],"from":[108,114,130,179,184,192],"0.88":[109],"0.94.":[111],"Specificity":[112],"0.92":[115],"0.95":[117],"types,":[121,175],"intersection":[123],"over":[124],"union":[125],"score":[126],"(IOU)":[127],"significantly":[129,189],"0.82":[131],"0.86":[133,185],"(p":[134,196],"&lt;":[135,197],"0.0001).":[136,198],"Human":[137],"LuN":[138],"biopsies":[139],"2":[142],"stained":[144],"markers":[149],"APC":[152],"markers,":[153],"separate":[155],"staining":[156],"panels":[157],"identify":[159],"different":[160],"APCs.":[163],"again":[166],"classification":[170],"increasing":[176,190],"overall":[177],"0.72":[180],"0.76,":[182],"specificity":[183],"0.93,":[187],"IOU":[191,200],"0.71":[193],"0.81":[195],"Improved":[199],"scores":[201],"are":[202],"particularly":[203],"important":[204],"CDM":[206],"be":[208],"able":[209],"quantify":[211],"shape":[213],"identification":[215],"functional":[217],"interactions":[218],"immune":[220,233,246],"is":[224],"therefore":[225],"superior":[227],"microscopy":[236],"images":[237],"image":[239],"analysis":[240],"cellular":[242],"function":[243],"pathological":[245],"states.":[247]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
