{"id":"https://openalex.org/W3155271616","doi":"https://doi.org/10.1109/access.2021.3073894","title":"Nuclei Detection for 3D Microscopy With a Fully Convolutional Regression Network","display_name":"Nuclei Detection for 3D Microscopy With a Fully Convolutional Regression Network","publication_year":2021,"publication_date":"2021-01-01","ids":{"openalex":"https://openalex.org/W3155271616","doi":"https://doi.org/10.1109/access.2021.3073894","mag":"3155271616","pmid":"https://pubmed.ncbi.nlm.nih.gov/35024261"},"language":"en","primary_location":{"id":"doi:10.1109/access.2021.3073894","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2021.3073894","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9312710/09406585.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/9312710/09406585.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066366331","display_name":"Maryse Lapierre-Landry","orcid":"https://orcid.org/0000-0002-9583-6876"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maryse Lapierre-Landry","raw_affiliation_strings":["Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA"],"raw_orcid":"https://orcid.org/0000-0002-9583-6876","affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018387904","display_name":"Zexuan Liu","orcid":"https://orcid.org/0000-0001-7463-1612"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zexuan Liu","raw_affiliation_strings":["Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003796962","display_name":"Shan Ling","orcid":"https://orcid.org/0000-0002-4160-3751"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shan Ling","raw_affiliation_strings":["Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066385395","display_name":"Mahdi Bayat","orcid":"https://orcid.org/0000-0001-9069-0823"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mahdi Bayat","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA"],"raw_orcid":"https://orcid.org/0000-0001-9069-0823","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059314323","display_name":"David L. Wilson","orcid":"https://orcid.org/0000-0001-9763-1463"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David L. Wilson","raw_affiliation_strings":["Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA","Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA"],"raw_orcid":"https://orcid.org/0000-0001-9763-1463","affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA","institution_ids":["https://openalex.org/I58956616"]},{"raw_affiliation_string":"Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086264408","display_name":"Michael W. Jenkins","orcid":"https://orcid.org/0000-0002-8908-5383"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael W. Jenkins","raw_affiliation_strings":["Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA","Department of Pediatrics, Case Western Reserve University, Cleveland, OH 44106, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA","institution_ids":["https://openalex.org/I58956616"]},{"raw_affiliation_string":"Department of Pediatrics, Case Western Reserve University, Cleveland, OH 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":2.4838,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.89641709,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"9","issue":null,"first_page":"60396","last_page":"60408"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9990000128746033,"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":0.9990000128746033,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/T10862","display_name":"AI in cancer detection","score":0.9900000095367432,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7053273320198059},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6701022386550903},{"id":"https://openalex.org/keywords/centroid","display_name":"Centroid","score":0.6551117300987244},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6545523405075073},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.6133593320846558},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5782921314239502},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.5537319779396057},{"id":"https://openalex.org/keywords/image-resolution","display_name":"Image resolution","score":0.45914149284362793},{"id":"https://openalex.org/keywords/image-segmentation","display_name":"Image segmentation","score":0.4107826054096222},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.32746729254722595}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7053273320198059},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6701022386550903},{"id":"https://openalex.org/C146599234","wikidata":"https://www.wikidata.org/wiki/Q511093","display_name":"Centroid","level":2,"score":0.6551117300987244},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6545523405075073},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.6133593320846558},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5782921314239502},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.5537319779396057},{"id":"https://openalex.org/C205372480","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"Image resolution","level":2,"score":0.45914149284362793},{"id":"https://openalex.org/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.4107826054096222},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.32746729254722595}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/access.2021.3073894","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2021.3073894","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9312710/09406585.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmid:35024261","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35024261","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":"IEEE access : practical innovations, open solutions","raw_type":null},{"id":"pmh:oai:doaj.org/article:74d3711d8530428996ec4efa009083a6","is_oa":true,"landing_page_url":"https://doaj.org/article/74d3711d8530428996ec4efa009083a6","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 9, Pp 60396-60408 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8751907","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8751907","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1109/access.2021.3073894","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2021.3073894","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9312710/09406585.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3641612026","display_name":null,"funder_award_id":"1OT2OD025307","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5102797004","display_name":null,"funder_award_id":"R01HL126747","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7148615917","display_name":null,"funder_award_id":"S10-OD024996","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7546798270","display_name":null,"funder_award_id":"20POST35220051/2020","funder_id":"https://openalex.org/F4320306230","funder_display_name":"American Heart Association"},{"id":"https://openalex.org/G8338946507","display_name":null,"funder_award_id":"20POST35220051","funder_id":"https://openalex.org/F4320306230","funder_display_name":"American Heart Association"}],"funders":[{"id":"https://openalex.org/F4320306230","display_name":"American Heart Association","ror":"https://ror.org/013kjyp64"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3155271616.pdf","grobid_xml":"https://content.openalex.org/works/W3155271616.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1524992328","https://openalex.org/W1533861849","https://openalex.org/W1901129140","https://openalex.org/W1973430870","https://openalex.org/W1976948919","https://openalex.org/W1978291928","https://openalex.org/W1990904097","https://openalex.org/W2034796052","https://openalex.org/W2091410499","https://openalex.org/W2093608864","https://openalex.org/W2127890285","https://openalex.org/W2130306094","https://openalex.org/W2137788460","https://openalex.org/W2167279371","https://openalex.org/W2257467030","https://openalex.org/W2293083603","https://openalex.org/W2296650473","https://openalex.org/W2312404985","https://openalex.org/W2345985845","https://openalex.org/W2347064614","https://openalex.org/W2550409828","https://openalex.org/W2595804542","https://openalex.org/W2738582428","https://openalex.org/W2744103196","https://openalex.org/W2788562687","https://openalex.org/W2792116521","https://openalex.org/W2829793374","https://openalex.org/W2891113118","https://openalex.org/W2900936384","https://openalex.org/W2906442564","https://openalex.org/W2911823761","https://openalex.org/W2960054497","https://openalex.org/W2961122344","https://openalex.org/W2961912654","https://openalex.org/W2962914239","https://openalex.org/W2964121744","https://openalex.org/W2991915699","https://openalex.org/W2996171578","https://openalex.org/W2998583117","https://openalex.org/W2999155059","https://openalex.org/W3000271566","https://openalex.org/W3004887924","https://openalex.org/W3028399772","https://openalex.org/W3080777683","https://openalex.org/W3093569261","https://openalex.org/W3094698871","https://openalex.org/W3120342826","https://openalex.org/W4250310729","https://openalex.org/W6631190155","https://openalex.org/W6679349572","https://openalex.org/W6734961017","https://openalex.org/W6773922849"],"related_works":["https://openalex.org/W2381926679","https://openalex.org/W2007009951","https://openalex.org/W2082644203","https://openalex.org/W2350539780","https://openalex.org/W3165040664","https://openalex.org/W4242386713","https://openalex.org/W4226493464","https://openalex.org/W3133861977","https://openalex.org/W2951211570","https://openalex.org/W3103566983"],"abstract_inverted_index":{"Advances":[0],"in":[1,44,62,100,123,152,204],"three-dimensional":[2,47,110],"microscopy":[3],"and":[4,15,34,46,60,73,80,119,142,144,169],"tissue":[5,131],"clearing":[6],"are":[7,20],"enabling":[8],"whole-organ":[9],"imaging":[10],"with":[11,97,106],"single-cell":[12],"resolution.":[13],"Fast":[14],"reliable":[16],"image":[17,26],"processing":[18],"tools":[19],"needed":[21],"to":[22,76,134,164],"analyze":[23],"the":[24,63,153,177,191],"resulting":[25,178],"volumes,":[27],"including":[28],"automated":[29],"cell":[30,32,35,140,209],"detection,":[31],"counting":[33],"analytics.":[36],"Deep":[37],"learning":[38],"approaches":[39],"have":[40],"shown":[41],"promising":[42],"results":[43],"two-":[45],"nuclei":[48,56,78,95,114,165,184],"detection":[49,115],"tasks,":[50],"however":[51],"detecting":[52],"overlapping":[53],"or":[54],"non-spherical":[55],"of":[57,65,117,137,166,183,194,208],"different":[58,125,167],"sizes":[59],"shapes":[61,168],"presence":[64],"a":[66,85,93,102,108,130],"blurring":[67],"point":[68],"spread":[69],"function":[70],"remains":[71],"challenging":[72],"often":[74],"leads":[75],"incorrect":[77],"merging":[79],"splitting.":[81],"Here":[82],"we":[83],"present":[84],"new":[86],"regression-based":[87],"fully":[88],"convolutional":[89],"network":[90],"that":[91,158,199],"located":[92],"thousand":[94],"centroids":[96],"high":[98,139,148],"accuracy":[99],"under":[101],"minute":[103],"when":[104],"combined":[105],"V-net,":[107],"popular":[109],"semantic-segmentation":[111],"architecture.":[112],"High":[113],"F1-scores":[116],"95.3%":[118],"92.5%":[120],"were":[121,150,174],"obtained":[122,151,185],"two":[124],"whole":[126],"quail":[127],"embryonic":[128],"hearts,":[129],"type":[132],"difficult":[133],"segment":[135],"because":[136],"its":[138],"density,":[141],"heterogeneous":[143],"elliptical":[145],"nuclei.":[146],"Similar":[147],"scores":[149],"mouse":[154],"brain":[155],"stem,":[156],"demonstrating":[157],"this":[159,200],"approach":[160,188,201],"is":[161],"highly":[162],"transferable":[163],"intensities.":[170],"Finally,":[171],"spatial":[172,181,192,206],"statistics":[173],"performed":[175],"on":[176],"centroids.":[179],"The":[180],"distribution":[182,193],"by":[186],"our":[187],"most":[189],"resembles":[190],"manually":[195],"identified":[196],"nuclei,":[197],"indicating":[198],"could":[202],"serve":[203],"future":[205],"analyses":[207],"organization.":[210]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":6}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
