{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T03:21:03Z","timestamp":1785295263237,"version":"3.55.0"},"reference-count":19,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2021,1,5]],"date-time":"2021-01-05T00:00:00Z","timestamp":1609804800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100009257","name":"ASN Foundation for Kidney Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009257","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"The National Cancer Institute","doi-asserted-by":"publisher","award":["1U01 CA239055\u201001"],"award-info":[{"award-number":["1U01 CA239055\u201001"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"The National Cancer Institute","doi-asserted-by":"publisher","award":["1U01 CA248226\u201001"],"award-info":[{"award-number":["1U01 CA248226\u201001"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"The National Cancer Institute","doi-asserted-by":"publisher","award":["1U24CA199374\u201001"],"award-info":[{"award-number":["1U24CA199374\u201001"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"The National Cancer Institute","doi-asserted-by":"publisher","award":["R01 CA216579\u201001A1"],"award-info":[{"award-number":["R01 CA216579\u201001A1"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"The National Cancer Institute","doi-asserted-by":"publisher","award":["R01 CA220581\u201001A1"],"award-info":[{"award-number":["R01 CA220581\u201001A1"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"The National Cancer Institute","doi-asserted-by":"publisher","award":["R01CA202752\u201001A1"],"award-info":[{"award-number":["R01CA202752\u201001A1"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"The National Cancer Institute","doi-asserted-by":"publisher","award":["R01CA208236\u201001A1"],"award-info":[{"award-number":["R01CA208236\u201001A1"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000097","name":"National Center for Research Resources","doi-asserted-by":"publisher","award":["1 C06 RR12463\u201001"],"award-info":[{"award-number":["1 C06 RR12463\u201001"]}],"id":[{"id":"10.13039\/100000097","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["R01\u2010DK\u2010118431."],"award-info":[{"award-number":["R01\u2010DK\u2010118431."]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["pathsocjournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Journal of Pathology"],"published-print":{"date-parts":[[2021,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Inconsistencies in the preparation of histology slides and whole\u2010slide images (WSIs) may lead to challenges with subsequent image analysis and machine learning approaches for interrogating the WSI. These variabilities are especially pronounced in multicenter cohorts, where batch effects (i.e. systematic technical artifacts unrelated to biological variability) may introduce biases to machine learning algorithms. To date, manual quality control (QC) has been the <jats:italic>de facto<\/jats:italic> standard for dataset curation, but remains highly subjective and is too laborious in light of the increasing scale of tissue slide digitization efforts. This study aimed to evaluate a computer\u2010aided QC pipeline for facilitating a reproducible QC process of WSI datasets. An open source tool, HistoQC, was employed to identify image artifacts and compute quantitative metrics describing visual attributes of WSIs to the Nephrotic Syndrome Study Network (NEPTUNE) digital pathology repository. A comparison in inter\u2010reader concordance between HistoQC aided and unaided curation was performed to quantify improvements in curation reproducibility. HistoQC metrics were additionally employed to quantify the presence of batch effects within NEPTUNE WSIs. Of the 1814 WSIs (458 H&amp;E, 470 PAS, 438 silver, 448 trichrome) from <jats:italic>n<\/jats:italic> =\u2009512 cases considered in this study, approximately 9% (163) were identified as unsuitable for subsequent computational analysis. The concordance in the identification of these WSIs among computational pathologists rose from moderate (Gwet's AC1 range 0.43 to 0.59 across stains) to excellent (Gwet's AC1 range 0.79 to 0.93 across stains) agreement when aided by HistoQC. Furthermore, statistically significant batch effects (<jats:italic>p<\/jats:italic> &lt;\u20090.001) in the NEPTUNE WSI dataset were discovered. Taken together, our findings strongly suggest that quantitative QC is a necessary step in the curation of digital pathology cohorts. \u00a9 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.<\/jats:p>","DOI":"10.1002\/path.5590","type":"journal-article","created":{"date-parts":[[2020,11,16]],"date-time":"2020-11-16T14:34:51Z","timestamp":1605537291000},"page":"268-278","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":64,"title":["Assessment of a computerized quantitative quality control tool for whole slide images of kidney biopsies"],"prefix":"10.1002","volume":"253","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3224-4339","authenticated-orcid":false,"given":"Yijiang","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering Case Western Reserve University  Cleveland OH USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jarcy","family":"Zee","sequence":"additional","affiliation":[{"name":"Arbor Research Collaborative for Health  Ann Arbor MI USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abigail","family":"Smith","sequence":"additional","affiliation":[{"name":"Arbor Research Collaborative for Health  Ann Arbor MI USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Jayapandian","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering Case Western Reserve University  Cleveland OH USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey","family":"Hodgin","sequence":"additional","affiliation":[{"name":"Department of Pathology University of Michigan  Ann Arbor MI USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Howell","sequence":"additional","affiliation":[{"name":"Department of Pathology Duke University  Durham NC USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Palmer","sequence":"additional","affiliation":[{"name":"Department of Pathology University of Pennsylvania  Philadelphia PA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Thomas","sequence":"additional","affiliation":[{"name":"Department of Pathology Duke University  Durham NC USA"},{"name":"Nephrocor  Memphis TN USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clarissa","family":"Cassol","sequence":"additional","affiliation":[{"name":"Renal Pathology Division Arkana Laboratories  Little Rock AK USA"},{"name":"Department of Pathology \u2010 Renal Pathology Division Ohio State University Medical Center  Columbus OH USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"III","given":"Alton B","family":"Farris","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine Emory University  Atlanta GA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn","family":"Perkinson","sequence":"additional","affiliation":[{"name":"Department of Pathology Duke University  Durham NC USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anant","family":"Madabhushi","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering Case Western Reserve University  Cleveland OH USA"},{"name":"Louis Stokes VA Medical Center  Cleveland OH USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Barisoni","sequence":"additional","affiliation":[{"name":"Department of Pathology Duke University  Durham NC USA"},{"name":"Department of Medicine, Division of Nephrology Duke University  Durham NC USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Janowczyk","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering Case Western Reserve University  Cleveland OH USA"},{"name":"Precision Oncology Center University of Lausanne  Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2021,1,5]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/ckj\/sfw129"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1177\/1040638718757582"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-bioeng-112415-114722"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.media.2016.06.037"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mjafi.2017.09.014"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1200\/CCI.18.00157"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty117"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/ki.2012.428"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.2215\/CJN.08370812"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.5858\/arpa.2017-0181-OA"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1002\/gepi.20516"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1002\/0471142905.hg0119s68"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.5b00780"},{"key":"e_1_2_7_15_1","unstructured":"GroundAI. MRQy: an open\u2010source tool for quality control of MR imaging data. [Accessed 8 July 2020]. Available from:https:\/\/www.groundai.com\/project\/mrqy-an-open-source-tool-for-quality-control-of-mr-imaging-data\/2"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw354"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1109\/TMI.2019.2919722"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1186\/1746-1596-8-S1-S23"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-41546-8_54"},{"key":"e_1_2_7_20_1","doi-asserted-by":"publisher","DOI":"10.1186\/1746-1596-9-S1-S3"}],"container-title":["The Journal of Pathology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/path.5590","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/path.5590","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/pathsocjournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/path.5590","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T16:15:30Z","timestamp":1761063330000},"score":1,"resource":{"primary":{"URL":"https:\/\/pathsocjournals.onlinelibrary.wiley.com\/doi\/10.1002\/path.5590"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,1,5]]},"references-count":19,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2021,3]]}},"alternative-id":["10.1002\/path.5590"],"URL":"https:\/\/doi.org\/10.1002\/path.5590","archive":["Portico"],"relation":{},"ISSN":["0022-3417","1096-9896"],"issn-type":[{"value":"0022-3417","type":"print"},{"value":"1096-9896","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,1,5]]},"assertion":[{"value":"2020-08-10","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2020-11-11","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-01-05","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}