{"id":"https://openalex.org/W4313452832","doi":"https://doi.org/10.1109/bibm55620.2022.9994861","title":"Tracing Randomly Oriented Filaments in a Simulated Actin Network Tomogram","display_name":"Tracing Randomly Oriented Filaments in a Simulated Actin Network Tomogram","publication_year":2022,"publication_date":"2022-12-06","ids":{"openalex":"https://openalex.org/W4313452832","doi":"https://doi.org/10.1109/bibm55620.2022.9994861","pmid":"https://pubmed.ncbi.nlm.nih.gov/40612327"},"language":"en","primary_location":{"id":"doi:10.1109/bibm55620.2022.9994861","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm55620.2022.9994861","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/12225917","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028410154","display_name":"Salim Sazzed","orcid":"https://orcid.org/0000-0002-8552-5337"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Salim Sazzed","raw_affiliation_strings":["Old Dominion University,Department of Computer Science,Norfolk,VA,23529"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Old Dominion University,Department of Computer Science,Norfolk,VA,23529","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069348801","display_name":"Peter Scheible","orcid":null},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter Scheible","raw_affiliation_strings":["Old Dominion University,Department of Computer Science,Norfolk,VA,23529"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Old Dominion University,Department of Computer Science,Norfolk,VA,23529","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049641499","display_name":"Jing He","orcid":"https://orcid.org/0000-0002-7249-4746"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jing He","raw_affiliation_strings":["Old Dominion University,Department of Computer Science,Norfolk,VA,23529"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Old Dominion University,Department of Computer Science,Norfolk,VA,23529","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010993930","display_name":"Willy Wriggers","orcid":"https://orcid.org/0000-0001-5326-3152"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Willy Wriggers","raw_affiliation_strings":["Old Dominion University,Department of Mechanical and Aerospace Engineering,Norfolk,VA,23529"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Old Dominion University,Department of Mechanical and Aerospace Engineering,Norfolk,VA,23529","institution_ids":["https://openalex.org/I81365321"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.46632124,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2022","issue":null,"first_page":"3486","last_page":"3491"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy 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/T10540","display_name":"Advanced Fluorescence Microscopy 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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9997000098228455,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9987999796867371,"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/protein-filament","display_name":"Protein filament","score":0.6775006651878357},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5671707391738892},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.5315508842468262},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.5113293528556824},{"id":"https://openalex.org/keywords/cartesian-coordinate-system","display_name":"Cartesian coordinate system","score":0.45617103576660156},{"id":"https://openalex.org/keywords/actin","display_name":"Actin","score":0.4501282870769501},{"id":"https://openalex.org/keywords/filopodia","display_name":"Filopodia","score":0.4360720217227936},{"id":"https://openalex.org/keywords/current","display_name":"Current (fluid)","score":0.41095688939094543},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3903278708457947},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.344961941242218},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32099902629852295},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.30356505513191223},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23853805661201477},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.19089791178703308},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18755418062210083},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.17503774166107178}],"concepts":[{"id":"https://openalex.org/C14228908","wikidata":"https://www.wikidata.org/wiki/Q2920483","display_name":"Protein filament","level":2,"score":0.6775006651878357},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5671707391738892},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.5315508842468262},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.5113293528556824},{"id":"https://openalex.org/C16038011","wikidata":"https://www.wikidata.org/wiki/Q62912","display_name":"Cartesian coordinate system","level":2,"score":0.45617103576660156},{"id":"https://openalex.org/C125705527","wikidata":"https://www.wikidata.org/wiki/Q185269","display_name":"Actin","level":2,"score":0.4501282870769501},{"id":"https://openalex.org/C90301020","wikidata":"https://www.wikidata.org/wiki/Q14859810","display_name":"Filopodia","level":3,"score":0.4360720217227936},{"id":"https://openalex.org/C148043351","wikidata":"https://www.wikidata.org/wiki/Q4456944","display_name":"Current (fluid)","level":2,"score":0.41095688939094543},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3903278708457947},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.344961941242218},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32099902629852295},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.30356505513191223},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23853805661201477},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.19089791178703308},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18755418062210083},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.17503774166107178},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bibm55620.2022.9994861","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm55620.2022.9994861","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmid:40612327","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40612327","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":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12225917","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12225917","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":"Proceedings (IEEE Int Conf Bioinformatics Biomed)","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:12225917","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12225917","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":"Proceedings (IEEE Int Conf Bioinformatics Biomed)","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320311672","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W2000894248","https://openalex.org/W2075641906","https://openalex.org/W2132629607","https://openalex.org/W2745375923","https://openalex.org/W2797054660","https://openalex.org/W2999706190","https://openalex.org/W3006546175","https://openalex.org/W4205141866","https://openalex.org/W4206504335","https://openalex.org/W4287010019"],"related_works":["https://openalex.org/W2969269896","https://openalex.org/W2615823300","https://openalex.org/W2740709913","https://openalex.org/W2009321415","https://openalex.org/W2950414472","https://openalex.org/W1975394131","https://openalex.org/W4387096203","https://openalex.org/W2045054874","https://openalex.org/W1965636754","https://openalex.org/W2085593975"],"abstract_inverted_index":{"filopodia":[0],"makes":[1],"identifying":[2,115],"filaments":[3],"within":[4,42],"noisy":[5,171],"cryo-electron":[6],"tomograms":[7],"extremely":[8],"challenging.":[9],"In":[10,142,156],"this":[11,198],"work,":[12],"we":[13,161],"present":[14],"a":[15,39,64,88,98,101,106,170,175,205,235],"computationally":[16],"efficient":[17],"dynamic":[18],"programming-based":[19],"framework":[20],"for":[21],"tracing":[22],"arbitrarily":[23],"oriented":[24],"actin":[25],"filaments.":[26],"Starting":[27],"from":[28],"locally":[29],"determined":[30],"seed":[31,73],"points,":[32],"it":[33,85,104],"accumulates":[34],"densities":[35,122],"along":[36],"paths":[37],"of":[38,44,100,117,137,166,184,195,204,223],"particular":[40],"length":[41],"45\u00b0":[43],"the":[45,75,78,132,144,150,157,164,167,182,202,216,221,224,240],"three":[46],"Cartesian":[47],"coordinate":[48],"axes.":[49],"This":[50],"novel":[51],"approach":[52],"covers":[53],"all":[54],"possible":[55],"orientations,":[56],"so":[57],"there":[58],"is":[59,82,94],"no":[60],"need":[61,229],"to":[62,96,139,148,153,211,230,233],"assume":[63],"dominant":[65],"direction":[66],"as":[67,87,218,220],"in":[68,239],"earlier":[69],"work.":[70],"For":[71],"each":[72],"point,":[74],"path":[76,108,121],"with":[77,119,174],"highest":[79],"density":[80,109],"value":[81],"selected,":[83],"and":[84,125,135],"acts":[86],"candidate":[89],"filament":[90,102,226],"segment":[91],"(CFS)":[92],"that":[93,179,228],"likely":[95],"form":[97],"part":[99],"when":[103],"has":[105],"high":[107,120],"value.":[110],"The":[111,128],"subsequent":[112],"stages":[113],"involve":[114],"groups":[116],"CFSs":[118,138,145],"by":[123],"binning":[124],"merging":[126,129,227],"them.":[127,141],"step":[130],"considers":[131],"relative":[133],"orientations":[134],"distances":[136],"connect":[140],"addition,":[143],"are":[146],"extended":[147],"fill":[149],"noise-induced":[151],"gaps":[152],"some":[154],"extent.":[155],"current":[158,225],"prototype":[159],"software,":[160],"focused":[162],"on":[163],"proof":[165],"concept,":[168],"using":[169],"simulated":[172],"tomogram":[173],"known":[176],"ground":[177],"truth":[178],"closely":[180],"mimics":[181],"appearance":[183],"an":[185,190],"experimental":[186],"map.":[187],"We":[188,214],"achieved":[189],"almost":[191],"perfect":[192],"precision":[193],"score":[194,208,238],"0.999,":[196],"but":[197],"success":[199],"came":[200],"at":[201],"expense":[203],"lower":[206],"recall":[207,237],"0.462":[209],"due":[210],"false":[212],"negatives.":[213],"discuss":[215],"dependencies":[217],"well":[219],"limitations":[222],"be":[231],"overcome":[232],"achieve":[234],"higher":[236],"future.":[241]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
