{"id":"https://openalex.org/W4214826628","doi":"https://doi.org/10.3389/fninf.2022.828169","title":"RealNeuralNetworks.jl: An Integrated Julia Package for Skeletonization, Morphological Analysis, and Synaptic Connectivity Analysis of Terabyte-Scale 3D Neural Segmentations","display_name":"RealNeuralNetworks.jl: An Integrated Julia Package for Skeletonization, Morphological Analysis, and Synaptic Connectivity Analysis of Terabyte-Scale 3D Neural Segmentations","publication_year":2022,"publication_date":"2022-03-02","ids":{"openalex":"https://openalex.org/W4214826628","doi":"https://doi.org/10.3389/fninf.2022.828169","pmid":"https://pubmed.ncbi.nlm.nih.gov/35311003"},"language":"en","primary_location":{"id":"doi:10.3389/fninf.2022.828169","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fninf.2022.828169","pdf_url":"https://www.frontiersin.org/articles/10.3389/fninf.2022.828169/pdf","source":{"id":"https://openalex.org/S179816892","display_name":"Frontiers in Neuroinformatics","issn_l":"1662-5196","issn":["1662-5196"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Neuroinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fninf.2022.828169/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047394906","display_name":"Jingpeng Wu","orcid":"https://orcid.org/0000-0003-1604-8802"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jingpeng Wu","raw_affiliation_strings":["Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States"],"affiliations":[{"raw_affiliation_string":"Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042520357","display_name":"Nicholas L. Turner","orcid":"https://orcid.org/0000-0001-5382-3420"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas Turner","raw_affiliation_strings":["Department of Computer Science, Princeton University, Princeton, NJ, United States","Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Princeton University, Princeton, NJ, United States","institution_ids":["https://openalex.org/I20089843"]},{"raw_affiliation_string":"Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100780771","display_name":"J. Alexander Bae","orcid":"https://orcid.org/0000-0002-4681-6342"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Alexander Bae","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ, United States","Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ, United States","institution_ids":["https://openalex.org/I20089843"]},{"raw_affiliation_string":"Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110577364","display_name":"Ashwin Vishwanathan","orcid":null},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ashwin Vishwanathan","raw_affiliation_strings":["Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States"],"affiliations":[{"raw_affiliation_string":"Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044273339","display_name":"H. Sebastian Seung","orcid":"https://orcid.org/0000-0002-8591-6733"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"H. Sebastian Seung","raw_affiliation_strings":["Department of Computer Science, Princeton University, Princeton, NJ, United States","Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Princeton University, Princeton, NJ, United States","institution_ids":["https://openalex.org/I20089843"]},{"raw_affiliation_string":"Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States","institution_ids":["https://openalex.org/I20089843"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5047394906"],"corresponding_institution_ids":["https://openalex.org/I20089843"],"apc_list":{"value":2950,"currency":"USD","value_usd":2950},"apc_paid":{"value":2950,"currency":"USD","value_usd":2950},"fwci":1.0223,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.81589958,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"16","issue":null,"first_page":"828169","last_page":"828169"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9944999814033508,"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":0.9944999814033508,"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/T10581","display_name":"Neural dynamics and brain function","score":0.9925000071525574,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10502","display_name":"Advanced Memory and Neural Computing","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/skeletonization","display_name":"Skeletonization","score":0.9476930499076843},{"id":"https://openalex.org/keywords/terabyte","display_name":"Terabyte","score":0.7355876564979553},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7352683544158936},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6319663524627686},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.5925303101539612},{"id":"https://openalex.org/keywords/connectomics","display_name":"Connectomics","score":0.5150894522666931},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4663023054599762},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.45139241218566895},{"id":"https://openalex.org/keywords/connectome","display_name":"Connectome","score":0.15108883380889893},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.13924512267112732},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.12666106224060059},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11870655417442322}],"concepts":[{"id":"https://openalex.org/C23951316","wikidata":"https://www.wikidata.org/wiki/Q1984140","display_name":"Skeletonization","level":2,"score":0.9476930499076843},{"id":"https://openalex.org/C199683683","wikidata":"https://www.wikidata.org/wiki/Q8799","display_name":"Terabyte","level":2,"score":0.7355876564979553},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7352683544158936},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6319663524627686},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.5925303101539612},{"id":"https://openalex.org/C2779097318","wikidata":"https://www.wikidata.org/wiki/Q2993446","display_name":"Connectomics","level":4,"score":0.5150894522666931},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4663023054599762},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.45139241218566895},{"id":"https://openalex.org/C45715564","wikidata":"https://www.wikidata.org/wiki/Q1292103","display_name":"Connectome","level":3,"score":0.15108883380889893},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.13924512267112732},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.12666106224060059},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11870655417442322},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"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}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fninf.2022.828169","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fninf.2022.828169","pdf_url":"https://www.frontiersin.org/articles/10.3389/fninf.2022.828169/pdf","source":{"id":"https://openalex.org/S179816892","display_name":"Frontiers in Neuroinformatics","issn_l":"1662-5196","issn":["1662-5196"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Neuroinformatics","raw_type":"journal-article"},{"id":"pmid:35311003","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35311003","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":"Frontiers in neuroinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:e12fb1afe90146b5ab7dda1b62dd8095","is_oa":true,"landing_page_url":"https://doaj.org/article/e12fb1afe90146b5ab7dda1b62dd8095","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Neuroinformatics, Vol 16 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8924549","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8924549","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Neuroinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fninf.2022.828169","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fninf.2022.828169","pdf_url":"https://www.frontiersin.org/articles/10.3389/fninf.2022.828169/pdf","source":{"id":"https://openalex.org/S179816892","display_name":"Frontiers in Neuroinformatics","issn_l":"1662-5196","issn":["1662-5196"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Neuroinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320333051","display_name":"Intelligence Advanced Research Projects Activity","ror":"https://ror.org/01v3fsc55"},{"id":"https://openalex.org/F4320337350","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320338281","display_name":"Army Research Office","ror":"https://ror.org/05epdh915"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4214826628.pdf","grobid_xml":"https://content.openalex.org/works/W4214826628.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1513082520","https://openalex.org/W1525852614","https://openalex.org/W1758641254","https://openalex.org/W1965210407","https://openalex.org/W1971354419","https://openalex.org/W1976111179","https://openalex.org/W1989396876","https://openalex.org/W1999149787","https://openalex.org/W2011650974","https://openalex.org/W2018227909","https://openalex.org/W2040156859","https://openalex.org/W2042967751","https://openalex.org/W2044648261","https://openalex.org/W2070468940","https://openalex.org/W2074633779","https://openalex.org/W2120575449","https://openalex.org/W2131683071","https://openalex.org/W2169528473","https://openalex.org/W2279313673","https://openalex.org/W2282666059","https://openalex.org/W2309258625","https://openalex.org/W2340082345","https://openalex.org/W2516230869","https://openalex.org/W2584383026","https://openalex.org/W2735195016","https://openalex.org/W2760861884","https://openalex.org/W2802399484","https://openalex.org/W2803596769","https://openalex.org/W2901860341","https://openalex.org/W2919115771","https://openalex.org/W2943035624","https://openalex.org/W2951976236","https://openalex.org/W2963659894","https://openalex.org/W2966778788","https://openalex.org/W2999635087","https://openalex.org/W3015332263","https://openalex.org/W3016007634","https://openalex.org/W3028116930","https://openalex.org/W3082752815","https://openalex.org/W3090744416","https://openalex.org/W3096661891","https://openalex.org/W3110215284","https://openalex.org/W3129175691","https://openalex.org/W3133640637","https://openalex.org/W3170256812","https://openalex.org/W3174415204","https://openalex.org/W3177792800","https://openalex.org/W3189506822","https://openalex.org/W4206755867","https://openalex.org/W4226227895","https://openalex.org/W4226228454","https://openalex.org/W6637764236","https://openalex.org/W6761601919","https://openalex.org/W6789871716","https://openalex.org/W6912612606","https://openalex.org/W6968900791","https://openalex.org/W6969169541","https://openalex.org/W7074132618"],"related_works":["https://openalex.org/W2132416234","https://openalex.org/W2118553688","https://openalex.org/W2092783742","https://openalex.org/W2292955152","https://openalex.org/W2376130299","https://openalex.org/W1549296799","https://openalex.org/W41790368","https://openalex.org/W2623093699","https://openalex.org/W2381976855","https://openalex.org/W2379187432"],"abstract_inverted_index":{"Benefiting":[0],"from":[1],"the":[2,29,73,89,120,131,134],"rapid":[3,86],"development":[4],"of":[5,16,28],"electron":[6,157],"microscopy":[7,158],"imaging":[8],"and":[9,22,62,70,81,107,140],"deep":[10],"learning":[11],"technologies,":[12],"an":[13],"increasing":[14],"number":[15],"brain":[17],"image":[18,159],"datasets":[19],"with":[20],"segmentation":[21,31,116,160],"synapse":[23],"detection":[24],"are":[25,54],"published.":[26],"Most":[27],"automated":[30],"methods":[32],"label":[33],"voxels":[34],"rather":[35],"than":[36],"producing":[37],"neuron":[38],"skeletons":[39],"directly.":[40],"A":[41],"further":[42],"skeletonization":[43,57,126],"step":[44],"is":[45,151],"necessary":[46],"for":[47,56,78,101,153],"quantitative":[48],"morphological":[49,61,105,138],"analysis.":[50,110],"Currently,":[51],"several":[52],"tools":[53],"published":[55],"as":[58,60],"well":[59],"synaptic":[63,108,141],"connectivity":[64,109,142],"analysis":[65],"using":[66,133],"different":[67],"computer":[68],"languages":[69],"environments.":[71],"Recently":[72],"Julia":[74,97],"programming":[75],"language,":[76],"notable":[77],"elegant":[79],"syntax":[80],"high":[82],"performance,":[83],"has":[84],"gained":[85],"adoption":[87],"in":[88,127,155],"scientific":[90],"computing":[91],"community.":[92],"Here,":[93],"we":[94,118],"present":[95],"a":[96,113],"package,":[98],"called":[99],"RealNeuralNetworks.jl,":[100],"efficient":[102],"sparse":[103],"skeletonization,":[104],"analysis,":[106],"Based":[111],"on":[112],"large-scale":[114],"Zebrafish":[115],"dataset,":[117],"illustrate":[119],"software":[121],"features":[122],"by":[123],"performing":[124],"distributed":[125],"Google":[128],"Cloud,":[129],"clustering":[130],"neurons":[132],"NBLAST":[135],"algorithm,":[136],"combining":[137],"similarity":[139],"to":[143],"study":[144],"their":[145],"relationship.":[146],"We":[147],"demonstrate":[148],"that":[149],"RealNeuralNetworks.jl":[150],"suitable":[152],"use":[154],"terabyte-scale":[156],"datasets.":[161]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}