{"id":"https://openalex.org/W4225748429","doi":"https://doi.org/10.1109/tmi.2022.3164343","title":"Scalable Biologically-Aware Skeleton Generation for Connectomic Volumes","display_name":"Scalable Biologically-Aware Skeleton Generation for Connectomic Volumes","publication_year":2022,"publication_date":"2022-04-04","ids":{"openalex":"https://openalex.org/W4225748429","doi":"https://doi.org/10.1109/tmi.2022.3164343","pmid":"https://pubmed.ncbi.nlm.nih.gov/35377840"},"language":"en","primary_location":{"id":"doi:10.1109/tmi.2022.3164343","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmi.2022.3164343","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/A5084050272","display_name":"Brian Matejek","orcid":"https://orcid.org/0000-0002-3517-9229"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian Matejek","raw_affiliation_strings":["School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0000-0002-3517-9229","affiliations":[{"raw_affiliation_string":"School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008712217","display_name":"Tim Franzmeyer","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Tim Franzmeyer","raw_affiliation_strings":["Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085365474","display_name":"Donglai Wei","orcid":"https://orcid.org/0000-0002-2329-5484"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Donglai Wei","raw_affiliation_strings":["School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073360935","display_name":"Xueying Wang","orcid":"https://orcid.org/0000-0002-2399-8083"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xueying Wang","raw_affiliation_strings":["Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0000-0002-2399-8083","affiliations":[{"raw_affiliation_string":"Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053626069","display_name":"Jinglin Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jinglin Zhao","raw_affiliation_strings":["Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034343681","display_name":"K\u00e1lm\u00e1n Pal\u00e1gyi","orcid":"https://orcid.org/0000-0002-3274-7315"},"institutions":[{"id":"https://openalex.org/I227486990","display_name":"University of Szeged","ror":"https://ror.org/01pnej532","country_code":"HU","type":"education","lineage":["https://openalex.org/I227486990"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Kalman Palagyi","raw_affiliation_strings":["Department of Image Processing and Computer Graphics, University of Szeged, Szeged, Hungary"],"raw_orcid":"https://orcid.org/0000-0002-3274-7315","affiliations":[{"raw_affiliation_string":"Department of Image Processing and Computer Graphics, University of Szeged, Szeged, Hungary","institution_ids":["https://openalex.org/I227486990"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037495122","display_name":"Jeff W. Lichtman","orcid":"https://orcid.org/0000-0002-0208-3212"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeff W. Lichtman","raw_affiliation_strings":["Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043151044","display_name":"Hanspeter Pfister","orcid":"https://orcid.org/0000-0002-3620-2582"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hanspeter Pfister","raw_affiliation_strings":["School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0000-0002-3620-2582","affiliations":[{"raw_affiliation_string":"School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4845,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.75843707,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"41","issue":"9","first_page":"2360","last_page":"2370"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9994999766349792,"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":0.9994999766349792,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9937999844551086,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9904000163078308,"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":0.807569146156311},{"id":"https://openalex.org/keywords/voxel","display_name":"Voxel","score":0.679593563079834},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.6149395108222961},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.601162850856781},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.538677990436554},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.488647997379303},{"id":"https://openalex.org/keywords/skeletonization","display_name":"Skeletonization","score":0.4833647608757019},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.47839128971099854},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.46171024441719055},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4340876042842865},{"id":"https://openalex.org/keywords/connectomics","display_name":"Connectomics","score":0.4126015901565552},{"id":"https://openalex.org/keywords/connectome","display_name":"Connectome","score":0.2822611331939697}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.807569146156311},{"id":"https://openalex.org/C54170458","wikidata":"https://www.wikidata.org/wiki/Q663554","display_name":"Voxel","level":2,"score":0.679593563079834},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.6149395108222961},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.601162850856781},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.538677990436554},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.488647997379303},{"id":"https://openalex.org/C23951316","wikidata":"https://www.wikidata.org/wiki/Q1984140","display_name":"Skeletonization","level":2,"score":0.4833647608757019},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.47839128971099854},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.46171024441719055},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4340876042842865},{"id":"https://openalex.org/C2779097318","wikidata":"https://www.wikidata.org/wiki/Q2993446","display_name":"Connectomics","level":4,"score":0.4126015901565552},{"id":"https://openalex.org/C45715564","wikidata":"https://www.wikidata.org/wiki/Q1292103","display_name":"Connectome","level":3,"score":0.2822611331939697},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"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":"D012863","descriptor_name":"Skeleton","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012863","descriptor_name":"Skeleton","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012863","descriptor_name":"Skeleton","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063132","descriptor_name":"Connectome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063132","descriptor_name":"Connectome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063132","descriptor_name":"Connectome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tmi.2022.3164343","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmi.2022.3164343","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:35377840","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35377840","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":[],"awards":[{"id":"https://openalex.org/G4613763048","display_name":null,"funder_award_id":"IIS-1607800","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W89176142","https://openalex.org/W255569507","https://openalex.org/W1486735428","https://openalex.org/W1501029715","https://openalex.org/W1520230096","https://openalex.org/W1901129140","https://openalex.org/W1973824709","https://openalex.org/W2007986094","https://openalex.org/W2014022174","https://openalex.org/W2026354831","https://openalex.org/W2045331793","https://openalex.org/W2048733914","https://openalex.org/W2064959667","https://openalex.org/W2107661883","https://openalex.org/W2112068711","https://openalex.org/W2143560481","https://openalex.org/W2146406922","https://openalex.org/W2146693559","https://openalex.org/W2158240273","https://openalex.org/W2163917985","https://openalex.org/W2232480453","https://openalex.org/W2267639398","https://openalex.org/W2293454490","https://openalex.org/W2464708700","https://openalex.org/W2529695649","https://openalex.org/W2560479124","https://openalex.org/W2592023542","https://openalex.org/W2596012030","https://openalex.org/W2598487345","https://openalex.org/W2619088528","https://openalex.org/W2623977141","https://openalex.org/W2625554823","https://openalex.org/W2754722056","https://openalex.org/W2760861884","https://openalex.org/W2893314438","https://openalex.org/W2900490697","https://openalex.org/W2901860341","https://openalex.org/W2949808130","https://openalex.org/W2950435239","https://openalex.org/W2979649602","https://openalex.org/W3014608058","https://openalex.org/W3016007634","https://openalex.org/W3044603806","https://openalex.org/W3090744416","https://openalex.org/W3109531692","https://openalex.org/W3170914969","https://openalex.org/W4309161063","https://openalex.org/W6738476636","https://openalex.org/W6744469682","https://openalex.org/W6775822003","https://openalex.org/W6796777449","https://openalex.org/W7055686756"],"related_works":["https://openalex.org/W2132416234","https://openalex.org/W2092783742","https://openalex.org/W2118553688","https://openalex.org/W2292955152","https://openalex.org/W2376130299","https://openalex.org/W2620696933","https://openalex.org/W4220907282","https://openalex.org/W2623093699","https://openalex.org/W1603323139","https://openalex.org/W1573128140"],"abstract_inverted_index":{"As":[0],"connectomic":[1],"datasets":[2],"exceed":[3],"hundreds":[4],"of":[5,14,24,76,79,94,162,190],"terabytes":[6],"in":[7],"size,":[8],"accurate":[9,48,108],"and":[10,33,110,155,165,170,177,208],"efficient":[11],"skeleton":[12],"generation":[13],"the":[15,25,66,77,88,124,134,184],"label":[16],"volumes":[17,53],"has":[18],"evolved":[19],"into":[20,187],"a":[21,38,74,99,115,137,149,188],"critical":[22],"component":[23],"computation":[26,191],"pipeline":[27],"used":[28],"for":[29,106,145],"analysis,":[30],"evaluation,":[31],"visualization,":[32],"error":[34],"correction.":[35],"We":[36,157,182,200],"propose":[37],"novel":[39],"topological":[40,139],"thinning":[41,140],"strategy":[42],"that":[43],"uses":[44],"biological-constraints":[45],"to":[46,65,101,129,133,196],"produce":[47],"centerlines":[49],"from":[50,87,123,211],"segmented":[51],"neuronal":[52],"while":[54],"still":[55],"maintaining":[56],"biologically":[57],"relevant":[58],"properties.":[59],"Current":[60],"methods":[61],"are":[62],"either":[63],"agnostic":[64],"underlying":[67],"biology,":[68],"have":[69],"non-linear":[70],"running":[71],"times":[72],"as":[73],"function":[75],"number":[78],"input":[80,89,125],"voxels,":[81],"or":[82],"both.":[83],"First,":[84],"we":[85],"eliminate":[86],"segmentation":[90,103],"biologically-infeasible":[91],"bubbles,":[92],"pockets":[93],"voxels":[95,219],"incorrectly":[96],"labeled":[97],"within":[98],"neuron,":[100],"improve":[102],"accuracy,":[104],"allow":[105],"more":[107],"centerlines,":[109],"increase":[111,197],"processing":[112,215],"speed.":[113],"Next,":[114],"Convolutional":[116],"Neural":[117],"Network":[118],"(CNN)":[119],"detects":[120],"cell":[121,171],"bodies":[122],"segmentation,":[126],"allowing":[127],"us":[128],"anchor":[130],"our":[131,202],"skeletons":[132,144],"somata.":[135],"Lastly,":[136],"synapse-aware":[138],"approach":[141],"produces":[142],"expressive":[143],"each":[146],"neuron":[147,209],"with":[148,224],"nearly":[150],"one-to-one":[151],"correspondence":[152],"between":[153,168],"endpoints":[154],"synapses.":[156],"simultaneously":[158],"estimate":[159],"geometric":[160],"properties":[161],"neurite":[163],"width":[164],"geodesic":[166],"distance":[167],"synapse":[169],"body,":[172],"improving":[173],"accuracy":[174],"by":[175],"47.5%":[176],"62.8%":[178],"over":[179,205,216],"baseline":[180],"methods.":[181],"separate":[183],"skeletonization":[185],"process":[186],"series":[189],"steps,":[192],"leveraging":[193],"data-parallel":[194],"strategies":[195],"throughput":[198],"significantly.":[199],"demonstrate":[201],"results":[203],"on":[204],"1250":[206],"neurons":[207],"fragments":[210],"three":[212],"different":[213],"species,":[214],"one":[217],"million":[218],"per":[220,222],"second":[221],"CPU":[223],"linear":[225],"scalability.":[226]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}