{"id":"https://openalex.org/W4387717474","doi":"https://doi.org/10.1109/tmi.2023.3323466","title":"NRTR: Neuron Reconstruction With Transformer From 3D Optical Microscopy Images","display_name":"NRTR: Neuron Reconstruction With Transformer From 3D Optical Microscopy Images","publication_year":2023,"publication_date":"2023-10-17","ids":{"openalex":"https://openalex.org/W4387717474","doi":"https://doi.org/10.1109/tmi.2023.3323466","pmid":"https://pubmed.ncbi.nlm.nih.gov/37847618"},"language":"en","primary_location":{"id":"doi:10.1109/tmi.2023.3323466","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/tmi.2023.3323466","pdf_url":null,"source":{"id":"https://openalex.org/S58069681","display_name":"IEEE Transactions on Medical Imaging","issn_l":"0278-0062","issn":["0278-0062","1558-254X"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Medical Imaging","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5100713690","display_name":"Yijun Wang","orcid":"https://orcid.org/0000-0002-1810-3994"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yijun Wang","raw_affiliation_strings":["School of Informatics, Xiamen University, Xiamen, China"],"affiliations":[{"raw_affiliation_string":"School of Informatics, Xiamen University, Xiamen, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103052046","display_name":"Rui Lang","orcid":"https://orcid.org/0009-0002-3444-0461"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Lang","raw_affiliation_strings":["School of Informatics, Xiamen University, Xiamen, China"],"affiliations":[{"raw_affiliation_string":"School of Informatics, Xiamen University, Xiamen, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100448663","display_name":"Rui Li","orcid":"https://orcid.org/0009-0001-4660-5430"},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Li","raw_affiliation_strings":["National Engineering Laboratory for Educational Big Data, Central China Normal University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"National Engineering Laboratory for Educational Big Data, Central China Normal University, Wuhan, China","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101641469","display_name":"Junsong Zhang","orcid":"https://orcid.org/0000-0002-7715-5006"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junsong Zhang","raw_affiliation_strings":["School of Informatics, Xiamen University, Xiamen, China"],"affiliations":[{"raw_affiliation_string":"School of Informatics, Xiamen University, Xiamen, China","institution_ids":["https://openalex.org/I191208505"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100713690"],"corresponding_institution_ids":["https://openalex.org/I191208505"],"apc_list":null,"apc_paid":null,"fwci":2.9195,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.91316346,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"43","issue":"2","first_page":"886","last_page":"898"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9998999834060669,"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":0.9998999834060669,"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/T13114","display_name":"Image Processing Techniques and Applications","score":0.9934999942779541,"subfield":{"id":"https://openalex.org/subfields/2214","display_name":"Media Technology"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9891999959945679,"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":0.7714035511016846},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6143766045570374},{"id":"https://openalex.org/keywords/tracing","display_name":"Tracing","score":0.5361231565475464},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5009422302246094},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.473732590675354},{"id":"https://openalex.org/keywords/biological-neuron-model","display_name":"Biological neuron model","score":0.46318742632865906},{"id":"https://openalex.org/keywords/iterative-reconstruction","display_name":"Iterative reconstruction","score":0.4623512029647827},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.42424309253692627},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.4127180874347687},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.39312857389450073},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.27984386682510376}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7714035511016846},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6143766045570374},{"id":"https://openalex.org/C138673069","wikidata":"https://www.wikidata.org/wiki/Q322229","display_name":"Tracing","level":2,"score":0.5361231565475464},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5009422302246094},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.473732590675354},{"id":"https://openalex.org/C186565885","wikidata":"https://www.wikidata.org/wiki/Q1651163","display_name":"Biological neuron model","level":3,"score":0.46318742632865906},{"id":"https://openalex.org/C141379421","wikidata":"https://www.wikidata.org/wiki/Q6094427","display_name":"Iterative reconstruction","level":2,"score":0.4623512029647827},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.42424309253692627},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.4127180874347687},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.39312857389450073},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.27984386682510376},{"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/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","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":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tmi.2023.3323466","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/tmi.2023.3323466","pdf_url":null,"source":{"id":"https://openalex.org/S58069681","display_name":"IEEE Transactions on Medical Imaging","issn_l":"0278-0062","issn":["0278-0062","1558-254X"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Medical Imaging","raw_type":"journal-article"},{"id":"pmid:37847618","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37847618","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 transactions on medical imaging","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4099999964237213,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G6050815528","display_name":null,"funder_award_id":"61772440","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6217570678","display_name":null,"funder_award_id":"62007016","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1502212269","https://openalex.org/W1508135620","https://openalex.org/W1901129140","https://openalex.org/W2018227909","https://openalex.org/W2047951563","https://openalex.org/W2092859932","https://openalex.org/W2124257654","https://openalex.org/W2194775991","https://openalex.org/W2222512263","https://openalex.org/W2256981962","https://openalex.org/W2404192493","https://openalex.org/W2565639579","https://openalex.org/W2594660495","https://openalex.org/W2884739365","https://openalex.org/W2910355434","https://openalex.org/W2912059704","https://openalex.org/W2925806435","https://openalex.org/W2962766617","https://openalex.org/W2979524214","https://openalex.org/W3001577996","https://openalex.org/W3035714866","https://openalex.org/W3042933035","https://openalex.org/W3096609285","https://openalex.org/W3126069796","https://openalex.org/W3134405878","https://openalex.org/W3160114960","https://openalex.org/W3182156280","https://openalex.org/W3212737625","https://openalex.org/W4214627427","https://openalex.org/W4225261422","https://openalex.org/W6629999756","https://openalex.org/W6631190155","https://openalex.org/W6738279954","https://openalex.org/W6739901393","https://openalex.org/W6763509872","https://openalex.org/W6784094891"],"related_works":["https://openalex.org/W2888673113","https://openalex.org/W2212288070","https://openalex.org/W2056065966","https://openalex.org/W2352602608","https://openalex.org/W2062641654","https://openalex.org/W3149975758","https://openalex.org/W4390516098","https://openalex.org/W1517786189","https://openalex.org/W1784583086","https://openalex.org/W2181948922"],"abstract_inverted_index":{"The":[0,101,128,138],"neuron":[1,19,29,49,76,99,121,126,159,181],"reconstruction":[2,30,50,77,160,182],"from":[3],"raw":[4,125],"Optical":[5],"Microscopy":[6],"(OM)":[7],"image":[8],"stacks":[9],"is":[10,45,90,141,176,183],"the":[11,54,71,84,91,106,131,151],"basis":[12],"of":[13,86,105,170],"neuroscience.":[14],"Manual":[15],"annotation":[16],"and":[17,24,58,111,153,165],"semi-automatic":[18],"tracing":[20],"algorithms":[21],"are":[22,133],"time-consuming":[23],"inefficient.":[25],"Existing":[26],"deep":[27,94],"learning":[28,95],"methods,":[31],"although":[32],"demonstrating":[33],"exemplary":[34],"performance,":[35],"greatly":[36],"demand":[37],"complex":[38,72],"rule-based":[39,73],"components.":[40],"Therefore,":[41],"a":[42,64,79,117,144,186],"crucial":[43],"challenge":[44],"designing":[46],"an":[47],"end-to-end":[48,98,191],"method":[51],"that":[52,174,180],"makes":[53,190],"overall":[55,102],"framework":[56],"simpler":[57],"model":[59,96,192],"training":[60,193],"easier.":[61],"We":[62],"propose":[63],"Neuron":[65],"Reconstruction":[66],"Transformer":[67,109],"(NRTR)":[68],"that,":[69],"discarding":[70],"components,":[74],"views":[75],"as":[78,143,185],"direct":[80],"set-prediction":[81,187],"problem.":[82],"To":[83],"best":[85],"our":[87],"knowledge,":[88],"NRTR":[89,115,156,175],"first":[92],"image-to-set":[93],"for":[97,124,162],"reconstruction.":[100],"pipeline":[103],"consists":[104],"CNN":[107],"backbone,":[108],"encoder-decoder,":[110],"connectivity":[112,136],"construction":[113],"module.":[114],"generates":[116],"point":[118,139],"set":[119,140],"representing":[120],"morphological":[122],"characteristics":[123],"images.":[127],"relationships":[129],"among":[130],"points":[132],"established":[134],"through":[135],"construction.":[137],"saved":[142],"standard":[145],"SWC":[146],"file.":[147],"In":[148],"experiments":[149,172],"using":[150],"BigNeuron":[152],"VISoR-40":[154],"datasets,":[155],"achieves":[157],"excellent":[158],"results":[161],"comprehensive":[163],"benchmarks":[164],"outperforms":[166],"competitive":[167],"baselines.":[168],"Results":[169],"extensive":[171],"indicate":[173],"effective":[177],"at":[178],"showing":[179],"viewed":[184],"problem,":[188],"which":[189],"available.":[194]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2026-02-28T09:26:25.869077","created_date":"2025-10-10T00:00:00"}