{"id":"https://openalex.org/W2947765342","doi":"https://doi.org/10.1101/655175","title":"An Automated 3D Analysis Framework for Optical Coherence Tomography Angiography","display_name":"An Automated 3D Analysis Framework for Optical Coherence Tomography Angiography","publication_year":2019,"publication_date":"2019-05-31","ids":{"openalex":"https://openalex.org/W2947765342","doi":"https://doi.org/10.1101/655175","mag":"2947765342"},"language":"en","primary_location":{"id":"doi:10.1101/655175","doi":"https://doi.org/10.1101/655175","is_oa":true,"landing_page_url":"https://doi.org/10.1101/655175","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/05/31/655175.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2019/05/31/655175.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052103441","display_name":"Mona Sharifi Sarabi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mona Sharifi Sarabi","raw_affiliation_strings":["USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, US","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039893847","display_name":"Jin Kyu Gahm","orcid":"https://orcid.org/0000-0001-8827-402X","observed_orcids":["https://orcid.org/0000-0001-8827-402X"]},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jin Kyu Gahm","raw_affiliation_strings":["USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, US","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049333841","display_name":"Maziyar M. Khansari","orcid":"https://orcid.org/0000-0001-9424-6754","observed_orcids":["https://orcid.org/0000-0001-9424-6754"]},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maziyar M. Khansari","raw_affiliation_strings":["USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine of University of Southern California, Los Angeles, CA, US","USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine of University of Southern California, Los Angeles, CA, US","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, US","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083371477","display_name":"Jiong Zhang","orcid":"https://orcid.org/0000-0002-1922-9118","observed_orcids":["https://orcid.org/0000-0002-1922-9118"]},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiong Zhang","raw_affiliation_strings":["USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine of University of Southern California, Los Angeles, CA, US","USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine of University of Southern California, Los Angeles, CA, US","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, US","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083998794","display_name":"Amir H. Kashani","orcid":"https://orcid.org/0000-0001-9767-7920","observed_orcids":["https://orcid.org/0000-0001-9767-7920"]},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amir H. Kashani","raw_affiliation_strings":["USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine of University of Southern California, Los Angeles, CA, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine of University of Southern California, Los Angeles, CA, US","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090261504","display_name":"Yonggang Shi","orcid":"https://orcid.org/0000-0002-3466-4302","observed_orcids":["https://orcid.org/0000-0002-3466-4302"]},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yonggang Shi","raw_affiliation_strings":["USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, US","institution_ids":["https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5090261504"],"corresponding_institution_ids":["https://openalex.org/I1174212"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11438","display_name":"Retinal Imaging and Analysis","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"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/T11438","display_name":"Retinal Imaging and Analysis","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"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/T11569","display_name":"Optical Coherence Tomography Applications","score":0.0013000000035390258,"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"}},{"id":"https://openalex.org/T10170","display_name":"Retinal Diseases and Treatments","score":0.0005000000237487257,"subfield":{"id":"https://openalex.org/subfields/2731","display_name":"Ophthalmology"},"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/optical-coherence-tomography-angiography","display_name":"optical coherence tomography angiography","score":0.9940000176429749},{"id":"https://openalex.org/keywords/retinal-capillaries","display_name":"retinal capillaries","score":0.8999999761581421},{"id":"https://openalex.org/keywords/diabetic-retinopathy","display_name":"diabetic retinopathy","score":0.9259999990463257},{"id":"https://openalex.org/keywords/capillary-density","display_name":"capillary density","score":0.8309999704360962},{"id":"https://openalex.org/keywords/retinal-vessel-network","display_name":"retinal vessel network","score":0.6000000238418579},{"id":"https://openalex.org/keywords/automated-image-analysis","display_name":"automated image analysis","score":0.6570000052452087}],"concepts":[{"id":"https://openalex.org/C2985858981","wikidata":"https://www.wikidata.org/wiki/Q60760969","display_name":"Optical coherence tomography angiography","level":3,"score":0.5975250601768494},{"id":"https://openalex.org/C57493831","wikidata":"https://www.wikidata.org/wiki/Q3134666","display_name":"Projection (relational algebra)","level":2,"score":0.5679817795753479},{"id":"https://openalex.org/C2779829184","wikidata":"https://www.wikidata.org/wiki/Q631361","display_name":"Diabetic retinopathy","level":3,"score":0.5105946660041809},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5037698149681091},{"id":"https://openalex.org/C2778818243","wikidata":"https://www.wikidata.org/wiki/Q899552","display_name":"Optical coherence tomography","level":2,"score":0.4477505683898926},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43482547998428345},{"id":"https://openalex.org/C2780827179","wikidata":"https://www.wikidata.org/wiki/Q422001","display_name":"Retinal","level":2,"score":0.4230867028236389},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.37889620661735535},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.29966408014297485},{"id":"https://openalex.org/C118487528","wikidata":"https://www.wikidata.org/wiki/Q161437","display_name":"Ophthalmology","level":1,"score":0.1623002588748932},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.10345906019210815},{"id":"https://openalex.org/C555293320","wikidata":"https://www.wikidata.org/wiki/Q12206","display_name":"Diabetes mellitus","level":2,"score":0.07904419302940369},{"id":"https://openalex.org/C134018914","wikidata":"https://www.wikidata.org/wiki/Q162606","display_name":"Endocrinology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/655175","doi":"https://doi.org/10.1101/655175","is_oa":true,"landing_page_url":"https://doi.org/10.1101/655175","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/05/31/655175.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/655175","doi":"https://doi.org/10.1101/655175","is_oa":true,"landing_page_url":"https://doi.org/10.1101/655175","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/05/31/655175.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"score":0.7246000170707703,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2947765342.pdf","grobid_xml":"https://content.openalex.org/works/W2947765342.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1480380503","https://openalex.org/W1570514300","https://openalex.org/W1762506961","https://openalex.org/W1932853004","https://openalex.org/W1966206262","https://openalex.org/W1976553652","https://openalex.org/W1977349774","https://openalex.org/W1981497401","https://openalex.org/W1986040035","https://openalex.org/W1992560794","https://openalex.org/W1996072235","https://openalex.org/W2018351099","https://openalex.org/W2032289033","https://openalex.org/W2032436926","https://openalex.org/W2033943996","https://openalex.org/W2052531822","https://openalex.org/W2069912449","https://openalex.org/W2070486213","https://openalex.org/W2096320880","https://openalex.org/W2105685332","https://openalex.org/W2110895006","https://openalex.org/W2115528090","https://openalex.org/W2127318120","https://openalex.org/W2127890285","https://openalex.org/W2129534965","https://openalex.org/W2133059825","https://openalex.org/W2133287637","https://openalex.org/W2164774194","https://openalex.org/W2259583284","https://openalex.org/W2291475016","https://openalex.org/W2317136217","https://openalex.org/W2462081900","https://openalex.org/W2518093818","https://openalex.org/W2526725142","https://openalex.org/W2579891345","https://openalex.org/W2594253297","https://openalex.org/W2609166709","https://openalex.org/W2737970336","https://openalex.org/W2741520251","https://openalex.org/W2743884226","https://openalex.org/W2758418434","https://openalex.org/W2769520760","https://openalex.org/W2775636951","https://openalex.org/W2976275745","https://openalex.org/W6658962014"],"related_works":["https://openalex.org/W3085288041","https://openalex.org/W2981600602","https://openalex.org/W4389561026","https://openalex.org/W2976275745","https://openalex.org/W7128484576","https://openalex.org/W7128438583","https://openalex.org/W4410550262","https://openalex.org/W4408567590","https://openalex.org/W4392552287","https://openalex.org/W1921052677"],"abstract_inverted_index":{"Abstract":[0],"Optical":[1],"Coherence":[2],"Tomography":[3],"Angiography":[4],"(OCTA)":[5],"is":[6,116,166],"a":[7,102,180],"novel,":[8],"non-invasive":[9],"imaging":[10],"modality":[11],"of":[12,47,66,89,104,171,193,227,232],"retinal":[13,48],"capillaries":[14],"at":[15],"micron":[16],"resolution.":[17],"While":[18],"OCTA":[19,67,106],"generates":[20],"3D":[21,40,64,90,134,162],"image":[22],"volumes,":[23],"current":[24],"analytic":[25],"methods":[26],"rely":[27],"on":[28,101],"2D":[29,151],"en":[30],"face":[31],"projection":[32,81,177],"images":[33],"for":[34,222],"quantitative":[35],"analysis.":[36],"This":[37,69,195],"obscures":[38],"the":[39,63,87,94,161,169,172,219,228],"vascular":[41],"geometry":[42,65],"and":[43,80,124,142,175,190,214,216],"prevents":[44],"accurate":[45],"characterization":[46],"vessel":[49,78,91,152],"networks.":[50],"In":[51,155],"this":[52,99],"paper,":[53],"we":[54,158],"have":[55],"developed":[56],"an":[57],"automated":[58],"analysis":[59],"framework":[60,70],"that":[61,133,146,160],"preserves":[62],"data.":[68],"uses":[71],"curvelet-based":[72],"denoising,":[73],"optimally":[74],"oriented":[75],"flux":[76],"(OOF)":[77],"enhancement":[79],"artifact":[82],"removal,":[83],"as":[84,86],"well":[85],"generation":[88],"length":[92],"from":[93,108,218],"Hamilton-Jacobi":[95],"skeleton.":[96],"We":[97],"implement":[98],"method":[100],"dataset":[103],"338":[105],"scans":[107],"human":[109],"subjects":[110],"with":[111],"diabetic":[112],"retinopathy":[113],"(DR)":[114],"which":[115,165],"known":[117],"to":[118,127,183,211],"cause":[119],"decrease":[120],"in":[121,139,150,199],"capillary":[122,144],"density":[123,145],"compare":[125],"them":[126],"healthy":[128,188],"controls.":[129],"Our":[130],"results":[131],"indicate":[132],"vessel-skeleton-length":[135],"(3D-VSL)":[136],"captures":[137],"differences":[138,186],"both":[140],"superficial":[141],"deep":[143],"are":[147],"not":[148],"apparent":[149],"skeleton":[153],"analyses.":[154],"statistical":[156],"analysis,":[157],"show":[159],"small-vessel-skeleton-length":[163],"(3D-SVSL),":[164],"computed":[167],"after":[168],"removal":[170],"large":[173],"vessels":[174],"associated":[176],"artifacts,":[178],"provides":[179],"novel":[181],"metric":[182],"detect":[184],"group":[185],"between":[187],"controls":[189],"progressive":[191],"stages":[192],"DR.":[194],"work":[196],"was":[197],"supported":[198],"part":[200],"by":[201],"NIH":[202],"grants":[203],"UH3NS100614,":[204],"R21EY027879,":[205],"U01EY025864,":[206],"K08EY027006,":[207],"P41EB015922,":[208],"P30EY029220,":[209],"Research":[210],"Prevent":[212],"Blindness,":[213],"UL1TR001855":[215],"UL1TR000130":[217],"National":[220,230],"Center":[221],"Advancing":[223],"Translational":[224],"Science":[225],"(NCATS)":[226],"U.S.":[229],"Institutes":[231],"Health.":[233]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-11-03T10:50:19.383937","created_date":"2019-06-07T00:00:00"}
