{"id":"https://openalex.org/W3129733638","doi":"https://doi.org/10.1117/12.2581247","title":"Correction of topological errors in automated traces of neurites","display_name":"Correction of topological errors in automated traces of neurites","publication_year":2021,"publication_date":"2021-02-13","ids":{"openalex":"https://openalex.org/W3129733638","doi":"https://doi.org/10.1117/12.2581247","mag":"3129733638","pmid":"https://pubmed.ncbi.nlm.nih.gov/33692606"},"language":"en","primary_location":{"id":"doi:10.1117/12.2581247","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2581247","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Medical Imaging 2021: Image Processing","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/7938329","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086762117","display_name":"Seyed Mostafa Mousavi Kahaki","orcid":"https://orcid.org/0000-0002-0249-3238"},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Seyed Mostafa Mousavi Kahaki","raw_affiliation_strings":["Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115, USA","Northeastern Univ. (United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Northeastern Univ. (United States)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101404356","display_name":"Hang Deng","orcid":"https://orcid.org/0000-0001-5784-996X"},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hang Deng","raw_affiliation_strings":["Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115, USA","Northeastern Univ. (United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Northeastern Univ. (United States)","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040846459","display_name":"Armen Stepanyants","orcid":"https://orcid.org/0000-0002-9387-2320"},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Armen Stepanyants","raw_affiliation_strings":["Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115, USA","Northeastern Univ. (United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Northeastern Univ. (United States)","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5086762117"],"corresponding_institution_ids":["https://openalex.org/I12912129"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00516707,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"11596","issue":null,"first_page":"58","last_page":"58"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9988999962806702,"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":0.9988999962806702,"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/T12536","display_name":"Topological and Geometric Data Analysis","score":0.9830999970436096,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9746999740600586,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7784042954444885},{"id":"https://openalex.org/keywords/connectomics","display_name":"Connectomics","score":0.7561625838279724},{"id":"https://openalex.org/keywords/trace","display_name":"TRACE (psycholinguistics)","score":0.5589743256568909},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5306790471076965},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5194544196128845},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.44170430302619934},{"id":"https://openalex.org/keywords/connectome","display_name":"Connectome","score":0.43833762407302856},{"id":"https://openalex.org/keywords/fidelity","display_name":"Fidelity","score":0.4202103614807129},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3959919810295105},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11545807123184204},{"id":"https://openalex.org/keywords/functional-connectivity","display_name":"Functional connectivity","score":0.11131051182746887}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7784042954444885},{"id":"https://openalex.org/C2779097318","wikidata":"https://www.wikidata.org/wiki/Q2993446","display_name":"Connectomics","level":4,"score":0.7561625838279724},{"id":"https://openalex.org/C75291252","wikidata":"https://www.wikidata.org/wiki/Q1315756","display_name":"TRACE (psycholinguistics)","level":2,"score":0.5589743256568909},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5306790471076965},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5194544196128845},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.44170430302619934},{"id":"https://openalex.org/C45715564","wikidata":"https://www.wikidata.org/wiki/Q1292103","display_name":"Connectome","level":3,"score":0.43833762407302856},{"id":"https://openalex.org/C2776459999","wikidata":"https://www.wikidata.org/wiki/Q2119376","display_name":"Fidelity","level":2,"score":0.4202103614807129},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3959919810295105},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11545807123184204},{"id":"https://openalex.org/C3018011982","wikidata":"https://www.wikidata.org/wiki/Q7316120","display_name":"Functional connectivity","level":2,"score":0.11131051182746887},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1117/12.2581247","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2581247","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Medical Imaging 2021: Image Processing","raw_type":"proceedings-article"},{"id":"pmid:33692606","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33692606","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:pubmedcentral.nih.gov:7938329","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7938329","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:7938329","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7938329","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"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":{"Our":[0],"understanding":[1],"of":[2,23,27,46,70,108,125,148,160,180,226],"synaptic":[3],"connectivity":[4],"in":[5,163,183,229,247],"the":[6,10,43,52,77,123,145,150,181,184,194,211,224,236,244,248],"brain":[7],"relies":[8],"on":[9,169],"ability":[11],"to":[12,102,116,143,175,235],"accurately":[13],"trace":[14,95,104],"sparsely":[15],"labeled":[16,119],"neurons":[17],"from":[18],"3D":[19],"optical":[20],"microscopy":[21],"stacks":[22,107],"images.":[24],"A":[25],"variety":[26],"automated":[28,94,230],"algorithms":[29,40],"and":[30,62,79,83,121,136,178,189,209,232],"software":[31],"tools":[32],"have":[33],"been":[34],"developed":[35],"for":[36,87,157,199,214],"this":[37],"task.":[38],"These":[39],"can":[41,74],"capture":[42],"general":[44],"layout":[45],"neurites":[47],"with":[48],"high":[49],"fidelity,":[50],"but":[51,173],"resulting":[53],"traces":[54,129,231],"often":[55],"contain":[56],"topological":[57,72,227],"errors":[58,73,228],"such":[59],"as":[60],"broken":[61],"incorrectly":[63],"merged":[64],"branches.":[65,151],"Even":[66],"a":[67,118,137,164,170,201],"small":[68],"number":[69,225],"isolated":[71],"drastically":[75],"alter":[76],"connectivity,":[78],"therefore,":[80],"their":[81],"detection":[82],"correction":[84],"are":[85],"paramount":[86],"connectomics":[88],"studies.":[89],"Here,":[90],"we":[91],"describe":[92],"an":[93],"proofreading":[96],"approach":[97],"that":[98,166,204],"utilizes":[99],"machine":[100],"learning":[101],"correct":[103,146],"topology.":[105],"Multiple":[106],"neuron":[109],"images":[110],"were":[111,130,155,197],"traced":[112],"by":[113,239],"two":[114],"users":[115,241],"create":[117],"dataset":[120],"assess":[122],"baseline":[124],"inter-user":[126],"variability.":[127],"All":[128],"then":[131],"disconnected":[132],"at":[133,193],"branch":[134,161,195,216],"points":[135],"deep":[138],"neural":[139,202],"network":[140,203],"was":[141],"trained":[142],"detect":[144],"way":[147,165],"reconnecting":[149],"Custom":[152],"morphological":[153],"features":[154,188],"generated":[156],"each":[158],"cluster":[159,182],"points,":[162],"is":[167,243],"dependent":[168],"merging":[171,217],"scenario":[172],"invariant":[174],"translations,":[176],"rotations,":[177],"reflections":[179],"imaging":[185],"plane.":[186],"The":[187,219],"image":[190],"volume":[191],"centered":[192],"point":[196],"used":[198],"training":[200],"concatenates":[205],"these":[206],"input":[207],"streams":[208],"outputs":[210],"confidence":[212],"measure":[213],"different":[215],"scenarios.":[218],"designed":[220],"method":[221],"significantly":[222],"reduces":[223],"comes":[233],"close":[234],"accuracy":[237],"achieved":[238],"expert":[240],"which":[242],"gold":[245],"standard":[246],"field.":[249]},"counts_by_year":[],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
