{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,5]],"date-time":"2026-11-05T07:27:15Z","timestamp":1793863635685,"version":"4.6.1"},"reference-count":55,"publisher":"Optica Publishing Group","issue":"5","license":[{"start":{"date-parts":[[2021,5,4]],"date-time":"2021-05-04T00:00:00Z","timestamp":1620086400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/doi.org\/10.1364\/OA_License_v1#VOR-OA"},{"start":{"date-parts":[[2021,5,4]],"date-time":"2021-05-04T00:00:00Z","timestamp":1620086400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/opg.optica.org\/policies\/opg-tdm-policy.json"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["K23-EY025014"],"award-info":[{"award-number":["K23-EY025014"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P30-EY005722"],"award-info":[{"award-number":["P30-EY005722"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01-EY018339"],"award-info":[{"award-number":["R01-EY018339"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01-EY029808"],"award-info":[{"award-number":["R01-EY029808"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01-EY030124"],"award-info":[{"award-number":["R01-EY030124"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R21-EY029804"],"award-info":[{"award-number":["R21-EY029804"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000038","name":"U.S. Food and Drug Administration","doi-asserted-by":"publisher","award":["A Critical Path Initiative (CPi) Grant"],"award-info":[{"award-number":["A Critical Path Initiative (CPi) Grant"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000038","name":"U.S. Food and Drug Administration","doi-asserted-by":"publisher","award":["FDA Critical Path Initiative (CPi) Grant"],"award-info":[{"award-number":["FDA Critical Path Initiative (CPi) Grant"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001818","name":"Research to Prevent Blindness","doi-asserted-by":"publisher","award":["Unrestricted to Duke Eye Center"],"award-info":[{"award-number":["Unrestricted to Duke Eye Center"]}],"id":[{"id":"10.13039\/100001818","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006792","name":"Hartwell Foundation","doi-asserted-by":"publisher","award":["Postdoctoral Fellowship"],"award-info":[{"award-number":["Postdoctoral Fellowship"]}],"id":[{"id":"10.13039\/100006792","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["opg.optica.org"],"crossmark-restriction":false},"short-container-title":["Optica"],"published-print":{"date-parts":[[2021,5,20]]},"abstract":"<jats:p>Cell-level quantitative features of retinal ganglion cells (GCs) are potentially important biomarkers for improved diagnosis and treatment monitoring of neurodegenerative diseases such as glaucoma, Parkinson\u2019s disease, and Alzheimer\u2019s disease. Yet, due to limited resolution, individual GCs cannot be visualized by commonly used ophthalmic imaging systems, including optical coherence tomography (OCT), and assessment is limited to gross layer thickness analysis. Adaptive optics OCT (AO-OCT) enables <jats:italic toggle=\"yes\">in vivo<\/jats:italic> imaging of individual retinal GCs. We present an automated segmentation of GC layer (GCL) somas from AO-OCT volumes based on weakly supervised deep learning (named WeakGCSeg), which effectively utilizes weak annotations in the training process. Experimental results show that WeakGCSeg is on par with or superior to human experts and is superior to other state-of-the-art networks. The automated quantitative features of individual GCLs show an increase in structure\u2013function correlation in glaucoma subjects compared to using thickness measures from OCT images. Our results suggest that by automatic quantification of GC morphology, WeakGCSeg can potentially alleviate a major bottleneck in using AO-OCT for vision research.<\/jats:p>","DOI":"10.1364\/optica.418274","type":"journal-article","created":{"date-parts":[[2021,3,24]],"date-time":"2021-03-24T21:00:07Z","timestamp":1616619607000},"page":"642","update-policy":"https:\/\/doi.org\/10.1364\/crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["Weakly supervised individual ganglion cell segmentation from adaptive\n\t\t\t\toptics OCT images for glaucomatous damage assessment"],"prefix":"10.1364","volume":"8","author":[{"given":"Somayyeh","family":"Soltanian-Zadeh","sequence":"first","affiliation":[{"name":"Duke University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuhiro","family":"Kurokawa","sequence":"additional","affiliation":[{"name":"Indiana University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8019-2054","authenticated-orcid":true,"given":"Zhuolin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Furu","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Osamah","family":"Saeedi","sequence":"additional","affiliation":[{"name":"University of Maryland Medical Center"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0532-1914","authenticated-orcid":true,"given":"Daniel X.","family":"Hammer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donald T.","family":"Miller","sequence":"additional","affiliation":[{"name":"Indiana University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4872-2902","authenticated-orcid":true,"given":"Sina","family":"Farsiu","sequence":"additional","affiliation":[{"name":"Duke University"},{"name":"Duke University Medical Center"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"285","published-online":{"date-parts":[[2021,5,4]]},"reference":[{"key":"optica-8-5-642-R1","doi-asserted-by":"publisher","first-page":"1711","DOI":"10.1016\/S0140-6736(04)16257-0","volume":"363","author":"Weinreb","year":"2004","journal-title":"Lancet"},{"key":"optica-8-5-642-R2","doi-asserted-by":"publisher","first-page":"1268","DOI":"10.1001\/archopht.120.10.1268","volume":"120","author":"Heijl","year":"2002","journal-title":"Arch. Ophthalmol."},{"key":"optica-8-5-642-R3","doi-asserted-by":"publisher","first-page":"1102","DOI":"10.1093\/oxfordjournals.aje.a116013","volume":"134","author":"Tielsch","year":"1991","journal-title":"Am. J. Epidemiol."},{"key":"optica-8-5-642-R4","doi-asserted-by":"publisher","first-page":"1234","DOI":"10.1167\/iovs.08-2535","volume":"50","author":"Tafreshi","year":"2009","journal-title":"Invest. Ophthalmol. Vis. Sci."},{"key":"optica-8-5-642-R5","first-page":"417","volume":"41","author":"Henson","year":"2000","journal-title":"Invest. Ophthalmol. Vis. Sci."},{"key":"optica-8-5-642-R6","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1016\/0002-9394(89)90006-8","volume":"108","author":"Heijl","year":"1989","journal-title":"Am. J. Ophthalmol."},{"key":"optica-8-5-642-R7","doi-asserted-by":"publisher","first-page":"S57","DOI":"10.1016\/j.ophtha.2017.07.015","volume":"124","author":"Tatham","year":"2017","journal-title":"Ophthalmology"},{"key":"optica-8-5-642-R8","doi-asserted-by":"publisher","first-page":"OCT556","DOI":"10.1167\/iovs.16-19933","volume":"57","author":"Dong","year":"2016","journal-title":"Invest. Ophthalmol. Vis. Sci."},{"key":"optica-8-5-642-R9","first-page":"19","volume":"25","author":"Ogden","year":"1984","journal-title":"Invest. Ophthalmol. Vis. Sci."},{"key":"optica-8-5-642-R10","doi-asserted-by":"publisher","first-page":"930","DOI":"10.1016\/j.ophtha.2016.01.041","volume":"123","author":"Banister","year":"2016","journal-title":"Ophthalmology"},{"key":"optica-8-5-642-R11","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1136\/bjophthalmol-2014-305745","volume":"99","author":"Mwanza","year":"2015","journal-title":"Br. J. Ophthalmol."},{"key":"optica-8-5-642-R12","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/j.ajo.2017.09.020","volume":"184","author":"Zhang","year":"2017","journal-title":"Am. J. Ophthalmol."},{"key":"optica-8-5-642-R13","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1016\/j.ophtha.2019.09.036","volume":"127","author":"Christopher","year":"2020","journal-title":"Ophthalmology"},{"key":"optica-8-5-642-R14","doi-asserted-by":"publisher","first-page":"3421","DOI":"10.1109\/JBHI.2020.3001019","volume":"24","author":"George","year":"2020","journal-title":"IEEE J. Biomed. Health Inf."},{"key":"optica-8-5-642-R15","doi-asserted-by":"publisher","first-page":"101695","DOI":"10.1016\/j.media.2020.101695","volume":"63","author":"Wang","year":"2020","journal-title":"Med. Image Anal."},{"key":"optica-8-5-642-R16","doi-asserted-by":"publisher","first-page":"12803","DOI":"10.1073\/pnas.1711734114","volume":"114","author":"Liu","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"optica-8-5-642-R17","doi-asserted-by":"publisher","first-page":"4246","DOI":"10.1364\/BOE.9.004246","volume":"9","author":"Liu","year":"2018","journal-title":"Biomed. Opt. Express"},{"key":"optica-8-5-642-R18","doi-asserted-by":"publisher","first-page":"1025","DOI":"10.1097\/IJG.0000000000001039","volume":"27","author":"Wells-Gray","year":"2018","journal-title":"J. Glaucoma"},{"key":"optica-8-5-642-R19","doi-asserted-by":"publisher","first-page":"586","DOI":"10.1073\/pnas.1613445114","volume":"114","author":"Rossi","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"optica-8-5-642-R20","doi-asserted-by":"publisher","first-page":"2732","DOI":"10.1364\/BOE.8.002732","volume":"8","author":"Fang","year":"2017","journal-title":"Biomed. Opt. Express"},{"key":"optica-8-5-642-R21","doi-asserted-by":"publisher","first-page":"5759","DOI":"10.1364\/BOE.9.005759","volume":"9","author":"Kugelman","year":"2018","journal-title":"Biomed. Opt. Express"},{"key":"optica-8-5-642-R22","doi-asserted-by":"publisher","first-page":"3627","DOI":"10.1364\/BOE.8.003627","volume":"8","author":"Roy","year":"2017","journal-title":"Biomed. Opt. Express"},{"key":"optica-8-5-642-R23","doi-asserted-by":"publisher","first-page":"1342","DOI":"10.1038\/s41591-018-0107-6","volume":"24","author":"De Fauw","year":"2018","journal-title":"Nat. Med."},{"key":"optica-8-5-642-R24","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1016\/j.media.2017.04.007","volume":"39","author":"Miri","year":"2017","journal-title":"Med. Image Anal."},{"key":"optica-8-5-642-R25","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1364\/BOE.9.001545","volume":"9","author":"Venhuizen","year":"2018","journal-title":"Biomed Opt. Express"},{"key":"optica-8-5-642-R26","doi-asserted-by":"publisher","first-page":"103445","DOI":"10.1016\/j.compbiomed.2019.103445","volume":"114","author":"Pekala","year":"2019","journal-title":"Comput. Biol. Med."},{"key":"optica-8-5-642-R27","doi-asserted-by":"publisher","first-page":"924","DOI":"10.1364\/BOE.4.000924","volume":"4","author":"Chiu","year":"2013","journal-title":"Biomed. Opt. Express"},{"key":"optica-8-5-642-R28","doi-asserted-by":"publisher","first-page":"7911","DOI":"10.1038\/s41598-018-26350-3","volume":"8","author":"Davidson","year":"2018","journal-title":"Sci. Rep."},{"key":"optica-8-5-642-R29","doi-asserted-by":"publisher","first-page":"5353","DOI":"10.1364\/BOE.9.005353","volume":"9","author":"Heisler","year":"2018","journal-title":"Biomed. Opt. Express"},{"key":"optica-8-5-642-R30","doi-asserted-by":"publisher","first-page":"3815","DOI":"10.1364\/BOE.10.003815","volume":"10","author":"Cunefare","year":"2019","journal-title":"Biomed. Opt. Express"},{"key":"optica-8-5-642-R31","first-page":"424","article-title":"3D U-Net: learning dense volumetric segmentation from sparse annotation","volume-title":"International Conference on Medical Image Computing and Computer-Assisted Intervention","author":"\u00c7i\u00e7ek","year":"2016"},{"key":"optica-8-5-642-R32","first-page":"565","article-title":"V-Net: fully convolutional neural networks for volumetric medical image segmentation","volume-title":"4th International Conference on 3D Vision (3DV)","author":"Milletari","year":"2016"},{"key":"optica-8-5-642-R33","doi-asserted-by":"publisher","first-page":"e172","DOI":"10.1016\/S2589-7500(19)30085-8","volume":"1","author":"Ran","year":"2019","journal-title":"Lancet Digital Health"},{"key":"optica-8-5-642-R34","doi-asserted-by":"publisher","first-page":"8554","DOI":"10.1073\/pnas.1812995116","volume":"116","author":"Soltanian-Zadeh","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"optica-8-5-642-R35","first-page":"618","article-title":"Grad-CAM: visual explanations from deep networks via gradient-based localization","volume-title":"IEEE International Conference on Computer Vision","author":"Selvaraju","year":"2017"},{"key":"optica-8-5-642-R36","first-page":"507","article-title":"On regularized losses for weakly-supervised cnn segmentation","volume-title":"European Conference on Computer Vision (ECCV)","author":"Tang","year":"2018"},{"key":"optica-8-5-642-R37","doi-asserted-by":"publisher","first-page":"19413","DOI":"10.1364\/OE.18.019413","volume":"18","author":"Chiu","year":"2010","journal-title":"Opt. Express"},{"key":"optica-8-5-642-R38","doi-asserted-by":"publisher","first-page":"1397","DOI":"10.1109\/TPAMI.2012.213","volume":"35","author":"He","year":"2012","journal-title":"IEEE Trans. Pattern Anal. Mach. Intell."},{"key":"optica-8-5-642-R39","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1007\/BF00175988","volume":"232","author":"Bennett","year":"1994","journal-title":"Graefe\u2019s Arch. Clin. Exp. Ophthalmol."},{"key":"optica-8-5-642-R40","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1016\/0197-4580(96)00010-3","volume":"17","author":"Blanks","year":"1996","journal-title":"Neurobiol. Aging"},{"key":"optica-8-5-642-R41","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1002\/cne.903000103","volume":"300","author":"Curcio","year":"1990","journal-title":"J. Comp. Neurol."},{"key":"optica-8-5-642-R42","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1097\/01.iae.0000238553.84036.3f","volume":"26","author":"Pavlidis","year":"2006","journal-title":"Retina"},{"key":"optica-8-5-642-R43","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1002\/cne.902330107","volume":"233","author":"Rodieck","year":"1985","journal-title":"J. Comp. Neurol."},{"key":"optica-8-5-642-R44","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1002\/cne.901960204","volume":"196","author":"Stone","year":"1981","journal-title":"J. Comp. Neurol."},{"key":"optica-8-5-642-R45","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1167\/iovs.62.3.34","volume":"62","author":"Liu","year":"2021","journal-title":"Invest. Ophthalmol. Vis. Sci."},{"key":"optica-8-5-642-R46","doi-asserted-by":"publisher","first-page":"1856","DOI":"10.1109\/TMI.2019.2959609","volume":"39","author":"Zhou","year":"2020","journal-title":"IEEE Trans. Med. Imaging"},{"key":"optica-8-5-642-R47","unstructured":"ZhouZ.SiddiqueeM. M. R.TajbakhshN.LiangJ., \u201cOfficial Keras implementation for UNet++,\u201d Github (2019), https:\/\/github.com\/MrGiovanni\/UNetPlusPlus."},{"key":"optica-8-5-642-R48","first-page":"1","volume":"7","author":"Dem\u0161ar","year":"2006","journal-title":"J. Mach. Learn. Res"},{"key":"optica-8-5-642-R49","first-page":"2677","volume":"9","author":"Garcia","year":"2008","journal-title":"J. Mach. Learn. Res."},{"key":"optica-8-5-642-R50","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1007\/978-3-319-17121-0_37","article-title":"Reliability and repeatability of cone density measurements in patients with congenital achromatopsia","volume-title":"Retinal Degenerative Diseases","author":"Abozaid","year":"2016"},{"key":"optica-8-5-642-R51","doi-asserted-by":"publisher","first-page":"2531","DOI":"10.1109\/TMI.2020.2973595","volume":"39","author":"Zhang","year":"2020","journal-title":"IEEE Trans. Med. Imaging"},{"key":"optica-8-5-642-R52","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.neuroimage.2019.03.026","volume":"194","author":"Perone","year":"2019","journal-title":"NeuroImage"},{"key":"optica-8-5-642-R53","doi-asserted-by":"publisher","first-page":"1562","DOI":"10.1109\/TMI.2018.2791721","volume":"37","author":"Wang","year":"2018","journal-title":"IEEE Trans. Med. Imaging"},{"key":"optica-8-5-642-R54","first-page":"11602","article-title":"Content-aware multi-level guidance for interactive instance segmentation","volume-title":"IEEE Conference on Computer Vision and Pattern Recognition","author":"Majumder","year":"2019"},{"key":"optica-8-5-642-R55","unstructured":"Soltanian-ZadehS.KurokawaK.LiuZ.ZhangF.SaeediO.HammerD. X.MillerD. T.FarsiuS., \u201c,\u201d Duke\n\t\t\t\t\tUniversity Repository (2021), http:\/\/people.duke.edu\/~sf59\/Soltanian_Optica_2021.htm."}],"container-title":["Optica"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/opg.optica.org\/viewmedia.cfm?URI=optica-8-5-642&seq=0","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T19:27:04Z","timestamp":1722972424000},"score":1,"resource":{"primary":{"URL":"https:\/\/opg.optica.org\/abstract.cfm?URI=optica-8-5-642"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,4]]},"references-count":55,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2021]]},"published-print":{"date-parts":[[2021]]}},"URL":"https:\/\/doi.org\/10.1364\/optica.418274","relation":{},"ISSN":["2334-2536"],"issn-type":[{"value":"2334-2536","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,5,4]]},"assertion":[{"value":"Optica Publishing Group","name":"publisher","label":"This article is maintained by"},{"value":"https:\/\/doi.org\/10.1364\/OPTICA.418274","name":"articlelink","label":"Crossref DOI link to publisher maintained version"},{"value":"research-article","name":"content_type","label":"Article type"},{"value":"Screened by Similarity Check","name":"cross_check","label":"Similarity check"},{"value":"Yes","order":0,"name":"peer_reviewed","label":"Peer reviewed","group":{"name":"peer_review","label":"Peer review"}},{"value":"Single blind","order":1,"name":"review_process","label":"Review process","group":{"name":"peer_review","label":"Peer review"}},{"value":"5 January 2021","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"23 March 2021","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"4 May 2021","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}},{"value":"\u00a9 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement","name":"copyright","label":"Copyright"}]}}