{"id":"https://openalex.org/W2007340698","doi":"https://doi.org/10.1145/2382936.2382958","title":"Automatic segmentation and quantification of filamentous structures in electron tomography","display_name":"Automatic segmentation and quantification of filamentous structures in electron tomography","publication_year":2012,"publication_date":"2012-10-07","ids":{"openalex":"https://openalex.org/W2007340698","doi":"https://doi.org/10.1145/2382936.2382958","mag":"2007340698","pmid":"https://pubmed.ncbi.nlm.nih.gov/28090597"},"language":"en","primary_location":{"id":"doi:10.1145/2382936.2382958","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2382936.2382958","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","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/5225986","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024523136","display_name":"Leandro A. Loss","orcid":null},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Leandro A. Loss","raw_affiliation_strings":["Lawrence Berkeley Nat Lab","Lawrence Berkeley Nat. Lab"],"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley Nat Lab","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Lawrence Berkeley Nat. Lab","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016844866","display_name":"George Bebis","orcid":"https://orcid.org/0000-0003-0966-6063"},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"George Bebis","raw_affiliation_strings":["University of Nevada, Reno"],"affiliations":[{"raw_affiliation_string":"University of Nevada, Reno","institution_ids":["https://openalex.org/I134113660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047619963","display_name":"Hang Chang","orcid":"https://orcid.org/0000-0002-3773-6818"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hang Chang","raw_affiliation_strings":["Lawrence Berkeley Nat Lab","Lawrence Berkeley Nat. Lab"],"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley Nat Lab","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Lawrence Berkeley Nat. Lab","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102846417","display_name":"Manfred Auer","orcid":"https://orcid.org/0000-0002-5435-9436"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manfred Auer","raw_affiliation_strings":["Univ of California, Berkeley","University of California, Berkeley"],"affiliations":[{"raw_affiliation_string":"Univ of California, Berkeley","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"University of California, Berkeley","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108204124","display_name":"Purbasha Sarkar","orcid":null},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Purbasha Sarkar","raw_affiliation_strings":["Univ of California, Berkeley","University of California, Berkeley"],"affiliations":[{"raw_affiliation_string":"Univ of California, Berkeley","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"University of California, Berkeley","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053749724","display_name":"Bahram Parvin","orcid":"https://orcid.org/0000-0002-6433-8006"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bahram Parvin","raw_affiliation_strings":["Lawrence Berkeley Nat Lab","Lawrence Berkeley Nat. Lab"],"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley Nat Lab","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Lawrence Berkeley Nat. Lab","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5024523136"],"corresponding_institution_ids":["https://openalex.org/I148283060"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.01924975,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"2012","issue":null,"first_page":"170","last_page":"177"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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"}},"topics":[{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T11786","display_name":"Geomagnetism and Paleomagnetism Studies","score":0.9761000275611877,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9648000001907349,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/hessian-matrix","display_name":"Hessian matrix","score":0.750329315662384},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.6200953722000122},{"id":"https://openalex.org/keywords/electron-tomography","display_name":"Electron tomography","score":0.6112502813339233},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5746565461158752},{"id":"https://openalex.org/keywords/tomography","display_name":"Tomography","score":0.5508841276168823},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.547137975692749},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4795474708080292},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.37636590003967285},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.2907566428184509},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.18443763256072998},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17531970143318176},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.1745246946811676},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.16871672868728638},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13204705715179443}],"concepts":[{"id":"https://openalex.org/C203616005","wikidata":"https://www.wikidata.org/wiki/Q620495","display_name":"Hessian matrix","level":2,"score":0.750329315662384},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.6200953722000122},{"id":"https://openalex.org/C75806775","wikidata":"https://www.wikidata.org/wiki/Q5358194","display_name":"Electron tomography","level":4,"score":0.6112502813339233},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5746565461158752},{"id":"https://openalex.org/C163716698","wikidata":"https://www.wikidata.org/wiki/Q841267","display_name":"Tomography","level":2,"score":0.5508841276168823},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.547137975692749},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4795474708080292},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.37636590003967285},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.2907566428184509},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.18443763256072998},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17531970143318176},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.1745246946811676},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.16871672868728638},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13204705715179443},{"id":"https://openalex.org/C146088050","wikidata":"https://www.wikidata.org/wiki/Q744818","display_name":"Transmission electron microscopy","level":2,"score":0.0},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C193016168","wikidata":"https://www.wikidata.org/wiki/Q874835","display_name":"Scanning transmission electron microscopy","level":3,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1145/2382936.2382958","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2382936.2382958","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},{"id":"pmid:28090597","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28090597","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":"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.299.911","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.299.911","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cse.unr.edu/~bebis/ACM_BCB_2012.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5225986","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5225986","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":"ACM BCB","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:5225986","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5225986","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":"ACM BCB","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3381946828","display_name":null,"funder_award_id":"P01 GM051487-15","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5659010513","display_name":null,"funder_award_id":"007G18","funder_id":"https://openalex.org/F4320309411","funder_display_name":"University of California Berkeley"},{"id":"https://openalex.org/G8145523722","display_name":null,"funder_award_id":"R01CA140663","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320309411","display_name":"University of California Berkeley","ror":"https://ror.org/01an7q238"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W84374482","https://openalex.org/W1525139902","https://openalex.org/W1555173571","https://openalex.org/W1575265895","https://openalex.org/W1975227291","https://openalex.org/W1977561071","https://openalex.org/W1978581225","https://openalex.org/W1981386238","https://openalex.org/W1991939713","https://openalex.org/W1992003716","https://openalex.org/W2008098614","https://openalex.org/W2017537431","https://openalex.org/W2020435927","https://openalex.org/W2029101220","https://openalex.org/W2036835491","https://openalex.org/W2042787006","https://openalex.org/W2048639106","https://openalex.org/W2096320880","https://openalex.org/W2109200236","https://openalex.org/W2121314950","https://openalex.org/W2122413595","https://openalex.org/W2132797060","https://openalex.org/W2142161929","https://openalex.org/W2344701987"],"related_works":["https://openalex.org/W1506774439","https://openalex.org/W1991282399","https://openalex.org/W3160864843","https://openalex.org/W4239081366","https://openalex.org/W2067552437","https://openalex.org/W1971214874","https://openalex.org/W1972392446","https://openalex.org/W2027708667","https://openalex.org/W4206515161","https://openalex.org/W4289333633"],"abstract_inverted_index":{"Electron":[0],"tomography":[1],"is":[2],"a":[3,32,46,118],"promising":[4],"technology":[5],"for":[6,50,99,143],"imaging":[7],"ultrastructures":[8],"at":[9],"nanoscale":[10],"resolutions.":[11],"However,":[12],"image":[13],"and":[14,27,44,53,78,89,109,149,161],"quantitative":[15],"analyses":[16,151],"are":[17],"often":[18],"hindered":[19],"by":[20,73],"high":[21],"levels":[22],"of":[23,34,55,65,71,83,92,101,106,120,133,152,164],"noise,":[24],"staining":[25],"heterogeneity,":[26],"material":[28],"damage":[29],"either":[30],"as":[31],"result":[33],"the":[35,93,153,162,165],"electron":[36,60],"beam":[37],"or":[38],"sample":[39],"preparation.":[40],"We":[41,112,125],"have":[42,138],"developed":[43],"built":[45],"framework":[47,130],"that":[48,137],"allows":[49,98],"automatic":[51],"segmentation":[52,129],"quantification":[54,100],"filamentous":[56,84,94,102],"objects":[57],"in":[58,104],"3D":[59],"tomography.":[61],"Our":[62,96],"approach":[63,97,116],"consists":[64],"three":[66],"steps:":[67],"(i)":[68],"local":[69],"enhancement":[70],"filaments":[72],"Hessian":[74],"filtering;":[75],"(ii)":[76],"detection":[77],"completion":[79],"(e.g.,":[80],"gap":[81],"filling)":[82],"structures":[85],"through":[86],"tensor":[87],"voting;":[88],"(iii)":[90],"delineation":[91],"networks.":[95],"networks":[103],"terms":[105],"their":[107,158],"compositional":[108,148],"morphological":[110,150],"features.":[111],"first":[113],"validate":[114],"our":[115,128],"using":[117],"set":[119],"specifically":[121],"designed":[122],"synthetic":[123],"data.":[124],"then":[126],"apply":[127],"to":[131],"tomograms":[132],"plant":[134,154],"cell":[135,155],"walls":[136,156],"undergone":[139],"different":[140,166],"chemical":[141,167],"treatments":[142],"polysaccharide":[144],"extraction.":[145],"The":[146],"subsequent":[147],"reveal":[157],"organizational":[159],"characteristics":[160],"effects":[163],"protocols":[168],"on":[169],"specific":[170],"polysaccharides.":[171]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
