{"id":"https://openalex.org/W2329032976","doi":"https://doi.org/10.1117/12.2216940","title":"Automated detection of retinal cell nuclei in 3D micro-CT images of zebrafish using support vector machine classification","display_name":"Automated detection of retinal cell nuclei in 3D micro-CT images of zebrafish using support vector machine classification","publication_year":2016,"publication_date":"2016-03-23","ids":{"openalex":"https://openalex.org/W2329032976","doi":"https://doi.org/10.1117/12.2216940","mag":"2329032976","pmid":"https://pubmed.ncbi.nlm.nih.gov/34548737"},"language":"en","primary_location":{"id":"doi:10.1117/12.2216940","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2216940","pdf_url":null,"source":{"id":"https://openalex.org/S183492911","display_name":"Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE","issn_l":"0277-786X","issn":["0277-786X","1996-756X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315543","host_organization_name":"SPIE","host_organization_lineage":["https://openalex.org/P4310315543"],"host_organization_lineage_names":["SPIE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SPIE Proceedings","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8452385","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037855655","display_name":"Yifu Ding","orcid":"https://orcid.org/0000-0002-4629-5858"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yifu Ding","raw_affiliation_strings":["Jake Gittlen Laboratories for Cancer Research and Department of Pathology, Penn State College of Medicine, Hershey, PA, USA 17033","Penn State College of Medicine (United States)"],"affiliations":[{"raw_affiliation_string":"Jake Gittlen Laboratories for Cancer Research and Department of Pathology, Penn State College of Medicine, Hershey, PA, USA 17033","institution_ids":[]},{"raw_affiliation_string":"Penn State College of Medicine (United States)","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045373968","display_name":"Thomas E. Tavolara","orcid":"https://orcid.org/0000-0001-6455-3120"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas Tavolara","raw_affiliation_strings":["Jake Gittlen Laboratories for Cancer Research and Department of Pathology, Penn State College of Medicine, Hershey, PA, USA 17033","Penn State College of Medicine (United States)"],"affiliations":[{"raw_affiliation_string":"Jake Gittlen Laboratories for Cancer Research and Department of Pathology, Penn State College of Medicine, Hershey, PA, USA 17033","institution_ids":[]},{"raw_affiliation_string":"Penn State College of Medicine (United States)","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079679570","display_name":"Keith C. Cheng","orcid":"https://orcid.org/0000-0002-5350-5825"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Keith Cheng","raw_affiliation_strings":["Jake Gittlen Laboratories for Cancer Research and Department of Pathology, Penn State College of Medicine, Hershey, PA, USA 17033","Penn State College of Medicine (United States)"],"affiliations":[{"raw_affiliation_string":"Jake Gittlen Laboratories for Cancer Research and Department of Pathology, Penn State College of Medicine, Hershey, PA, USA 17033","institution_ids":[]},{"raw_affiliation_string":"Penn State College of Medicine (United States)","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5037855655"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.00972953,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"9791","issue":null,"first_page":"97911A","last_page":"97911A"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11438","display_name":"Retinal Imaging and Analysis","score":0.9883999824523926,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.7409748435020447},{"id":"https://openalex.org/keywords/zebrafish","display_name":"Zebrafish","score":0.5966529846191406},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5904847383499146},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5699477791786194},{"id":"https://openalex.org/keywords/phenome","display_name":"Phenome","score":0.5413913130760193},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.5061396956443787},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.43669217824935913},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41643229126930237},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4055846333503723},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.38337209820747375},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3729953169822693},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.3255463242530823}],"concepts":[{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.7409748435020447},{"id":"https://openalex.org/C2776878037","wikidata":"https://www.wikidata.org/wiki/Q169444","display_name":"Zebrafish","level":3,"score":0.5966529846191406},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5904847383499146},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5699477791786194},{"id":"https://openalex.org/C7952369","wikidata":"https://www.wikidata.org/wiki/Q844116","display_name":"Phenome","level":4,"score":0.5413913130760193},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.5061396956443787},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.43669217824935913},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41643229126930237},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4055846333503723},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.38337209820747375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3729953169822693},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.3255463242530823},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1117/12.2216940","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2216940","pdf_url":null,"source":{"id":"https://openalex.org/S183492911","display_name":"Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE","issn_l":"0277-786X","issn":["0277-786X","1996-756X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315543","host_organization_name":"SPIE","host_organization_lineage":["https://openalex.org/P4310315543"],"host_organization_lineage_names":["SPIE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SPIE Proceedings","raw_type":"proceedings-article"},{"id":"pmid:34548737","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34548737","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of SPIE--the International Society for Optical Engineering","raw_type":null},{"id":"pmh:oai:europepmc.org:7343239","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8452385","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8452385","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8452385","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc SPIE Int Soc Opt Eng","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8452385","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8452385","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc SPIE Int Soc Opt Eng","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1481523241","https://openalex.org/W1971167172","https://openalex.org/W1981323832","https://openalex.org/W2006030184","https://openalex.org/W2014022579","https://openalex.org/W2017625145","https://openalex.org/W2024986448","https://openalex.org/W2087338534","https://openalex.org/W2105201875","https://openalex.org/W2157150618","https://openalex.org/W2161969291","https://openalex.org/W4206679801","https://openalex.org/W4239510810","https://openalex.org/W4250039758","https://openalex.org/W4255056905"],"related_works":["https://openalex.org/W3129642199","https://openalex.org/W4256528904","https://openalex.org/W1597543017","https://openalex.org/W3009438210","https://openalex.org/W3037132967","https://openalex.org/W3010444534","https://openalex.org/W3157580922","https://openalex.org/W4290380913","https://openalex.org/W4386776929","https://openalex.org/W2947302526"],"abstract_inverted_index":{"Our":[0],"group":[1],"is":[2,65,102,179],"developing":[3],"a":[4,98,123,156],"method":[5,17],"to":[6,32,75,93,104,159,166,180,186],"examine":[7,160],"biological":[8],"specimens":[9],"in":[10,35,137,142,170],"cellular":[11,57,182],"detail":[12],"using":[13],"synchrotron":[14],"microCT.":[15],"The":[16,173],"can":[18,163],"acquire":[19],"3D":[20,143],"images":[21,96,144],"of":[22,38,53,91,95,114,132,145,176,197],"tissue":[23,54,184],"at":[24,194],"micrometer-scale":[25],"resolutions,":[26],"allowing":[27],"for":[28,67,97,110,190],"individual":[29],"cell":[30,140],"types":[31],"be":[33,164,187],"visualized":[34],"the":[36,39,50,88,111,130,152,195,198],"context":[37],"entire":[40],"specimen.":[41],"For":[42],"model":[43],"organism":[44,115],"research,":[45],"this":[46,177],"tool":[47],"will":[48],"enable":[49],"rapid":[51],"characterization":[52,64],"architecture":[55],"and":[56,69,79,183],"morphology":[58,185],"from":[59,82],"every":[60],"organ":[61,118,192],"system.":[62],"This":[63],"critical":[66],"proposed":[68],"ongoing":[70],"\"phenome\"":[71],"projects":[72],"that":[73,127],"aim":[74],"phenotype":[76],"whole-organism":[77],"mutants":[78],"diseased":[80],"tissues":[81],"different":[83],"organisms":[84],"including":[85],"humans.":[86],"With":[87],"envisioned":[89],"collection":[90],"hundreds":[92],"thousands":[94],"phenome":[99],"project,":[100],"it":[101],"important":[103],"develop":[105],"quantitative":[106],"image":[107],"analysis":[108],"tools":[109],"automated":[112],"scoring":[113],"phenotypes":[116],"across":[117],"systems.":[119],"Here":[120],"we":[121,150],"present":[122],"first":[124],"step":[125],"towards":[126],"goal,":[128],"demonstrating":[129],"use":[131],"support":[133],"vector":[134],"machines":[135],"(SVM)":[136],"detecting":[138],"retinal":[139],"nuclei":[141],"wild-type":[146],"zebrafish.":[147],"In":[148],"addition,":[149],"apply":[151],"SVM":[153],"classifier":[154],"on":[155],"mutant":[157],"zebrafish":[158],"whether":[161],"SVMs":[162],"used":[165],"capture":[167],"phenotypic":[168],"differences":[169],"these":[171],"images.":[172],"long-term":[174],"goal":[175],"work":[178],"allow":[181],"characterized":[188],"quantitatively":[189],"many":[191],"systems,":[193],"level":[196],"whole-organism.":[199]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}