{"id":"https://openalex.org/W4386352583","doi":"https://doi.org/10.1109/isbi53787.2023.10230745","title":"High Throughput Deep Model of 3D Nucleus Instance Segmentation by Stereo Stitching Contextual Gaps","display_name":"High Throughput Deep Model of 3D Nucleus Instance Segmentation by Stereo Stitching Contextual Gaps","publication_year":2023,"publication_date":"2023-04-18","ids":{"openalex":"https://openalex.org/W4386352583","doi":"https://doi.org/10.1109/isbi53787.2023.10230745"},"language":"en","primary_location":{"id":"doi:10.1109/isbi53787.2023.10230745","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/isbi53787.2023.10230745","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112992192","display_name":"Ziquan Wei","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ziquan Wei","raw_affiliation_strings":["University of North Carolina at Chapel Hill,Departments of Psychiatry,Chapel Hill,NC,USA","Departments of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill,Departments of Psychiatry,Chapel Hill,NC,USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Departments of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088548858","display_name":"Tingting Dan","orcid":"https://orcid.org/0000-0001-6936-2649"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tingting Dan","raw_affiliation_strings":["University of North Carolina at Chapel Hill,Departments of Psychiatry,Chapel Hill,NC,USA","Departments of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill,Departments of Psychiatry,Chapel Hill,NC,USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Departments of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061485017","display_name":"Jiaqi Ding","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiaqi Ding","raw_affiliation_strings":["University of North Carolina at Chapel Hill,Computer Science,Chapel Hill,NC,USA","Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill,Computer Science,Chapel Hill,NC,USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067301510","display_name":"Carolyn M. McCormick","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carolyn McCormick","raw_affiliation_strings":["University of North Carolina at Chapel Hill,Genetics,Chapel Hill,NC,USA","Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill,Genetics,Chapel Hill,NC,USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005113165","display_name":"Felix A. Kyere","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Felix A. Kyere","raw_affiliation_strings":["University of North Carolina at Chapel Hill,Genetics,Chapel Hill,NC,USA","UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill,Genetics,Chapel Hill,NC,USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100416234","display_name":"Minjeong Kim","orcid":"https://orcid.org/0009-0004-7712-1684"},"institutions":[{"id":"https://openalex.org/I169335092","display_name":"University of North Carolina at Greensboro","ror":"https://ror.org/04fnxsj42","country_code":"US","type":"education","lineage":["https://openalex.org/I169335092"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Minjeong Kim","raw_affiliation_strings":["University of North Carolina at Greensboro,Department of Computer Science,Greensboro,NC,USA","Department of Computer Science, University of North Carolina at Greensboro, Greensboro, NC, USA"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Greensboro,Department of Computer Science,Greensboro,NC,USA","institution_ids":["https://openalex.org/I169335092"]},{"raw_affiliation_string":"Department of Computer Science, University of North Carolina at Greensboro, Greensboro, NC, USA","institution_ids":["https://openalex.org/I169335092"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001966756","display_name":"David Borland","orcid":"https://orcid.org/0000-0002-0162-4080"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I69048370","display_name":"Renaissance Computing Institute","ror":"https://ror.org/01s91ey96","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535","https://openalex.org/I170897317","https://openalex.org/I69048370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Borland","raw_affiliation_strings":["University of North Carolina at Chapel Hill,RENCI,Chapel Hill,NC,USA","RENCI, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill,RENCI,Chapel Hill,NC,USA","institution_ids":["https://openalex.org/I114027177","https://openalex.org/I69048370"]},{"raw_affiliation_string":"RENCI, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177","https://openalex.org/I69048370"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011912522","display_name":"Jason L. Stein","orcid":"https://orcid.org/0000-0003-4829-0513"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason L. Stein","raw_affiliation_strings":["University of North Carolina at Chapel Hill,Genetics,Chapel Hill,NC,USA","UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill,Genetics,Chapel Hill,NC,USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021809690","display_name":"Guorong Wu","orcid":"https://orcid.org/0000-0002-0550-6145"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guorong Wu","raw_affiliation_strings":["University of North Carolina at Chapel Hill,Departments of Psychiatry,Chapel Hill,NC,USA","UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","Departments of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill,Departments of Psychiatry,Chapel Hill,NC,USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Departments of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5112992192"],"corresponding_institution_ids":["https://openalex.org/I114027177"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10172704,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"43","issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10627","display_name":"Advanced Image and Video Retrieval Techniques","score":0.9980000257492065,"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"}},"topics":[{"id":"https://openalex.org/T10627","display_name":"Advanced Image and Video Retrieval Techniques","score":0.9980000257492065,"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/T10052","display_name":"Medical Image Segmentation Techniques","score":0.9976999759674072,"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/T10036","display_name":"Advanced Neural Network Applications","score":0.9970999956130981,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/image-stitching","display_name":"Image stitching","score":0.8692041039466858},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.7956959009170532},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.7388575077056885},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6781154870986938},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.621661365032196},{"id":"https://openalex.org/keywords/voxel","display_name":"Voxel","score":0.5190580487251282},{"id":"https://openalex.org/keywords/nucleus","display_name":"Nucleus","score":0.48902663588523865},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.44387489557266235},{"id":"https://openalex.org/keywords/3d-model","display_name":"3d model","score":0.42624717950820923},{"id":"https://openalex.org/keywords/connectomics","display_name":"Connectomics","score":0.41646403074264526},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4137961268424988},{"id":"https://openalex.org/keywords/connectome","display_name":"Connectome","score":0.31330978870391846},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.2154974341392517},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14718440175056458}],"concepts":[{"id":"https://openalex.org/C29081049","wikidata":"https://www.wikidata.org/wiki/Q1364242","display_name":"Image stitching","level":2,"score":0.8692041039466858},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.7956959009170532},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7388575077056885},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6781154870986938},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.621661365032196},{"id":"https://openalex.org/C54170458","wikidata":"https://www.wikidata.org/wiki/Q663554","display_name":"Voxel","level":2,"score":0.5190580487251282},{"id":"https://openalex.org/C2780723820","wikidata":"https://www.wikidata.org/wiki/Q1934178","display_name":"Nucleus","level":2,"score":0.48902663588523865},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.44387489557266235},{"id":"https://openalex.org/C3019007443","wikidata":"https://www.wikidata.org/wiki/Q568742","display_name":"3d model","level":2,"score":0.42624717950820923},{"id":"https://openalex.org/C2779097318","wikidata":"https://www.wikidata.org/wiki/Q2993446","display_name":"Connectomics","level":4,"score":0.41646403074264526},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4137961268424988},{"id":"https://openalex.org/C45715564","wikidata":"https://www.wikidata.org/wiki/Q1292103","display_name":"Connectome","level":3,"score":0.31330978870391846},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.2154974341392517},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14718440175056458},{"id":"https://openalex.org/C3018011982","wikidata":"https://www.wikidata.org/wiki/Q7316120","display_name":"Functional connectivity","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/isbi53787.2023.10230745","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/isbi53787.2023.10230745","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W3021714323","https://openalex.org/W3035442500","https://openalex.org/W3042513075","https://openalex.org/W3099064910","https://openalex.org/W3111521801","https://openalex.org/W3132455321","https://openalex.org/W3164139555","https://openalex.org/W3167292670","https://openalex.org/W3202801842","https://openalex.org/W3203815210","https://openalex.org/W4229377239","https://openalex.org/W4292828884","https://openalex.org/W6810502309"],"related_works":["https://openalex.org/W3210800206","https://openalex.org/W1744057168","https://openalex.org/W2124698428","https://openalex.org/W2091472861","https://openalex.org/W2945607120","https://openalex.org/W2086448982","https://openalex.org/W112425480","https://openalex.org/W2550381304","https://openalex.org/W2946138627","https://openalex.org/W3112117434"],"abstract_inverted_index":{"Whole-brain":[0],"three":[1],"dimensional":[2],"(3D)":[3],"nucleus":[4,98,126,143,210],"instance":[5,99,144,211,232],"segmentation":[6,92,100,134,145,212,233],"is":[7,50,71,180,186,235],"vital":[8],"to":[9,25,53,74,132,188],"quantify":[10],"regional":[11],"variations":[12],"in":[13,37,43,64,79,102,119,231],"many":[14],"neuroscience":[15],"studies":[16],"using":[17],"tissue":[18],"clearing":[19],"and":[20,82,137,245],"microscopy":[21,31,215],"imaging":[22],"technologies.":[23],"Due":[24],"the":[26,65,90,142,190,197,202,239],"large":[27],"size":[28,110],"of":[29,97,117,147,204,217],"whole-brain":[30,91],"images":[32,216],"(\u03bcm":[33],"vs.":[34],"mm":[35],"resolution":[36],"MRI":[38],"leads":[39],"voxel":[40],"volume":[41],"increasing":[42],"10<sup":[44],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[45],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">9</sup>":[46],"level),":[47],"however,":[48],"it":[49,70],"computationally":[51],"challenging":[52],"train":[54],"an":[55],"end-to-end":[56],"deep":[57,113,150,170],"model":[58,184,207,224],"that":[59],"can":[60,164],"recognize":[61],"nuclei":[62,118],"instances":[63,78],"full":[66],"3D":[67,87,209],"volume.":[68],"Instead,":[69],"common":[72],"practice":[73],"first":[75],"segment":[76],"2D":[77,125,194],"each":[80,106],"slice":[81],"then":[83],"assemble":[84],"them":[85],"into":[86,168,225],"instances.":[88],"Moreover,":[89],"often":[93],"comprises":[94],"a":[95,108,158,175,181,228],"collection":[96],"results":[101],"pre-partitioned":[103],"image":[104],"stacks,":[105],"with":[107],"manageable":[109],"for":[111,208],"applying":[112],"models.":[114,151],"Complex":[115],"arrangements":[116],"close":[120],"proximity":[121],"makes":[122],"stitching":[123,161,206,223],"together":[124],"segmentations":[127,195],"across":[128,242],"slices":[129,244],"non-trivial,":[130],"leading":[131],"inconsistent":[133],"along":[135,196],"inter-slice":[136],"cross-stack":[138],"gaps,":[139],"which":[140,163,185],"undermines":[141],"accuracy":[146,234],"current":[148],"state-of-the-art":[149],"To":[152],"address":[153],"this":[154],"challenge":[155],"we":[156],"present":[157],"flexible":[159],"learning-based":[160],"component":[162],"be":[165],"either":[166],"integrated":[167],"existing":[169,226],"models":[171],"or":[172],"used":[173],"as":[174],"post-processing":[176],"step.":[177],"The":[178],"backbone":[179],"contextual":[182],"graph":[183],"trained":[187],"predict":[189],"one-to-one":[191],"correspondence":[192],"between":[193],"gap.":[198],"We":[199],"have":[200],"evaluated":[201],"performance":[203],"our":[205,222],"from":[213],"light-sheet":[214],"mouse":[218],"brains.":[219],"After":[220],"integrating":[221],"methods,":[227],"significant":[229],"improvement":[230],"achieved":[236],"by":[237],"alleviating":[238],"inconsistency":[240],"issue":[241],"discontinuous":[243],"stacks.":[246]},"counts_by_year":[],"updated_date":"2025-12-21T01:58:51.020947","created_date":"2025-10-10T00:00:00"}