{"id":"https://openalex.org/W3206008729","doi":"https://doi.org/10.1093/bioinformatics/btab716","title":"Neuron segmentation using 3D wavelet integrated encoder\u2013decoder network","display_name":"Neuron segmentation using 3D wavelet integrated encoder\u2013decoder network","publication_year":2021,"publication_date":"2021-10-12","ids":{"openalex":"https://openalex.org/W3206008729","doi":"https://doi.org/10.1093/bioinformatics/btab716","mag":"3206008729","pmid":"https://pubmed.ncbi.nlm.nih.gov/34647994"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab716","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab716","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/3/809/42167487/btab716.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/3/809/42167487/btab716.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074364531","display_name":"Qiufu Li","orcid":"https://orcid.org/0000-0002-8120-6531"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiufu Li","raw_affiliation_strings":["AI Research Center for Medical Image Analysis and Diagnosis, Shenzhen University , Shenzhen 518060, China","Computer Vision Institute, College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China","Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen University , Shenzhen 518060, China"],"raw_orcid":"https://orcid.org/0000-0002-8120-6531","affiliations":[{"raw_affiliation_string":"AI Research Center for Medical Image Analysis and Diagnosis, Shenzhen University , Shenzhen 518060, China","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"Computer Vision Institute, College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen University , Shenzhen 518060, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019313200","display_name":"Linlin Shen","orcid":"https://orcid.org/0000-0003-1420-0815"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Linlin Shen","raw_affiliation_strings":["AI Research Center for Medical Image Analysis and Diagnosis, Shenzhen University , Shenzhen 518060, China","Computer Vision Institute, College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China","Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen University , Shenzhen 518060, China","Marshall Laboratory of Biomedical Engineering, Shenzhen University, Shenzhen 518060, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Research Center for Medical Image Analysis and Diagnosis, Shenzhen University , Shenzhen 518060, China","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"Computer Vision Institute, College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen University , Shenzhen 518060, China","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"Marshall Laboratory of Biomedical Engineering, Shenzhen University, Shenzhen 518060, China","institution_ids":["https://openalex.org/I180726961"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5019313200"],"corresponding_institution_ids":["https://openalex.org/I180726961"],"apc_list":{"value":3478,"currency":"USD","value_usd":3478},"apc_paid":{"value":3478,"currency":"USD","value_usd":3478},"fwci":2.5625,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.90061384,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"38","issue":"3","first_page":"809","last_page":"817"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.972599983215332,"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":0.972599983215332,"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/T10036","display_name":"Advanced Neural Network Applications","score":0.00430000014603138,"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":0.0035000001080334187,"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/segmentation","display_name":"Segmentation","score":0.812000036239624},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.796825647354126},{"id":"https://openalex.org/keywords/neuron","display_name":"Neuron","score":0.5884076356887817},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5682976245880127},{"id":"https://openalex.org/keywords/biological-neuron-model","display_name":"Biological neuron model","score":0.5404483079910278},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.5074893832206726},{"id":"https://openalex.org/keywords/tracing","display_name":"Tracing","score":0.50608891248703},{"id":"https://openalex.org/keywords/wavelet","display_name":"Wavelet","score":0.48871588706970215},{"id":"https://openalex.org/keywords/connectomics","display_name":"Connectomics","score":0.4589875638484955},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4223543405532837},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.3952119052410126},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.24213141202926636},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.12342575192451477},{"id":"https://openalex.org/keywords/connectome","display_name":"Connectome","score":0.10027828812599182}],"concepts":[{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.812000036239624},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.796825647354126},{"id":"https://openalex.org/C2778794669","wikidata":"https://www.wikidata.org/wiki/Q43054","display_name":"Neuron","level":2,"score":0.5884076356887817},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5682976245880127},{"id":"https://openalex.org/C186565885","wikidata":"https://www.wikidata.org/wiki/Q1651163","display_name":"Biological neuron model","level":3,"score":0.5404483079910278},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.5074893832206726},{"id":"https://openalex.org/C138673069","wikidata":"https://www.wikidata.org/wiki/Q322229","display_name":"Tracing","level":2,"score":0.50608891248703},{"id":"https://openalex.org/C47432892","wikidata":"https://www.wikidata.org/wiki/Q831390","display_name":"Wavelet","level":2,"score":0.48871588706970215},{"id":"https://openalex.org/C2779097318","wikidata":"https://www.wikidata.org/wiki/Q2993446","display_name":"Connectomics","level":4,"score":0.4589875638484955},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4223543405532837},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.3952119052410126},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.24213141202926636},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.12342575192451477},{"id":"https://openalex.org/C45715564","wikidata":"https://www.wikidata.org/wiki/Q1292103","display_name":"Connectome","level":3,"score":0.10027828812599182},{"id":"https://openalex.org/C3018011982","wikidata":"https://www.wikidata.org/wiki/Q7316120","display_name":"Functional connectivity","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab716","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab716","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/3/809/42167487/btab716.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34647994","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34647994","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8756182","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8756182","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab716","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab716","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/3/809/42167487/btab716.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3292400719","display_name":null,"funder_award_id":"62006156","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8985577795","display_name":null,"funder_award_id":"91959108","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3206008729.pdf","grobid_xml":"https://content.openalex.org/works/W3206008729.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1508135620","https://openalex.org/W1926682734","https://openalex.org/W2016277672","https://openalex.org/W2017478274","https://openalex.org/W2018227909","https://openalex.org/W2036901575","https://openalex.org/W2051036306","https://openalex.org/W2061186544","https://openalex.org/W2076507262","https://openalex.org/W2124257654","https://openalex.org/W2146842127","https://openalex.org/W2153965609","https://openalex.org/W2156114286","https://openalex.org/W2158940042","https://openalex.org/W2256981962","https://openalex.org/W2404192493","https://openalex.org/W2494923364","https://openalex.org/W2554820184","https://openalex.org/W2594660495","https://openalex.org/W2618167249","https://openalex.org/W2746403246","https://openalex.org/W2904533595","https://openalex.org/W2913693872","https://openalex.org/W2929906481","https://openalex.org/W2952846208","https://openalex.org/W2955111813","https://openalex.org/W2957395818","https://openalex.org/W2963881378","https://openalex.org/W2966593583","https://openalex.org/W3035714866","https://openalex.org/W3083599814","https://openalex.org/W6766740334"],"related_works":["https://openalex.org/W4287673583","https://openalex.org/W3083399682","https://openalex.org/W3093145634","https://openalex.org/W3178259930","https://openalex.org/W1769982787","https://openalex.org/W3184949856","https://openalex.org/W2320160082","https://openalex.org/W4281997648","https://openalex.org/W3099906890","https://openalex.org/W3035839890"],"abstract_inverted_index":{"MOTIVATION:":[0],"3D":[1,68,73,94,98,146,193,201],"neuron":[2,10,31,45,74,178,186,202],"segmentation":[3,75,89,179,203],"is":[4,14,80,163],"a":[5,35,67,130],"key":[6],"step":[7],"for":[8,16,212],"the":[9,25,44,48,59,88,96,105,109,111,115,124,136,149,159,184,198],"digital":[11],"reconstruction,":[12],"which":[13,38,162],"essential":[15],"exploring":[17],"brain":[18,22],"circuits":[19],"and":[20,51,70,122,204,210],"understanding":[21],"functions.":[23],"However,":[24],"fine":[26],"line-shaped":[27],"nerve":[28,53,106,150],"fibers":[29,54,107,151],"of":[30,200],"could":[32,113,181],"spread":[33],"in":[34,108,118,153,187],"large":[36],"region,":[37],"brings":[39],"great":[40,56],"computational":[41],"cost":[42],"to":[43,58,86,103,144,157],"segmentation.":[46],"Meanwhile,":[47],"strong":[49],"noises":[50,121],"disconnected":[52],"bring":[55],"challenges":[57],"task.":[60,90],"RESULTS:":[61],"In":[62],"this":[63,213],"article,":[64],"we":[65,92],"propose":[66],"wavelet":[69,99],"deep":[71,116],"learning-based":[72],"method.":[76],"The":[77,172,191,208],"neuronal":[78,84,140,189],"image":[79,141],"first":[81,97],"partitioned":[82],"into":[83],"cubes":[85,154],"simplify":[87],"Then,":[91],"design":[93],"WaveUNet,":[95],"integrated":[100,192],"encoder-decoder":[101],"network,":[102],"segment":[104],"cubes;":[110],"wavelets":[112,194],"assist":[114],"networks":[117],"suppressing":[119],"data":[120,209,222],"connecting":[123],"broken":[125],"fibers.":[126],"We":[127],"also":[128],"produce":[129],"Neuronal":[131],"Cube":[132],"Dataset":[133],"(NeuCuDa)":[134],"using":[135,166],"biggest":[137],"available":[138,168,216,224],"annotated":[139],"dataset,":[142],"BigNeuron,":[143],"train":[145],"WaveUNet.":[147],"Finally,":[148],"segmented":[152],"are":[155,215,223],"assembled":[156],"generate":[158],"complete":[160],"neuron,":[161],"digitally":[164],"reconstructed":[165],"an":[167],"automatic":[169],"tracing":[170],"algorithm.":[171],"experimental":[173],"results":[174],"show":[175],"that":[176],"our":[177],"method":[180],"completely":[182],"extract":[183],"target":[185],"noisy":[188],"images.":[190],"can":[195],"efficiently":[196],"improve":[197],"performance":[199],"reconstruction.":[205],"AVAILABILITYAND":[206],"IMPLEMENTATION:":[207],"codes":[211],"work":[214],"at":[217,225],"https://github.com/LiQiufu/3D-WaveUNet.":[218],"SUPPLEMENTARY":[219],"INFORMATION:":[220],"Supplementary":[221],"Bioinformatics":[226],"online.":[227]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2}],"updated_date":"2026-09-04T10:56:28.161419","created_date":"2025-10-10T00:00:00"}
