{"id":"https://openalex.org/W3006546175","doi":"https://doi.org/10.1021/acs.jcim.9b01111","title":"Correction of Missing-Wedge Artifacts in Filamentous Tomograms by Template-Based Constrained Deconvolution","display_name":"Correction of Missing-Wedge Artifacts in Filamentous Tomograms by Template-Based Constrained Deconvolution","publication_year":2020,"publication_date":"2020-02-11","ids":{"openalex":"https://openalex.org/W3006546175","doi":"https://doi.org/10.1021/acs.jcim.9b01111","mag":"3006546175","pmid":"https://pubmed.ncbi.nlm.nih.gov/32045242"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b01111","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01111","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-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/8279804","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068517610","display_name":"Julio Kovacs","orcid":"https://orcid.org/0000-0002-1829-7119"},"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":"Julio Kovacs","raw_affiliation_strings":["Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089234257","display_name":"Junha Song","orcid":"https://orcid.org/0000-0003-2015-1749"},"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":"Junha Song","raw_affiliation_strings":["Cell and Tissue Imaging, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California 94720, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cell and Tissue Imaging, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California 94720, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102846417","display_name":"Manfred Auer","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":false,"raw_author_name":"Manfred Auer","raw_affiliation_strings":["Cell and Tissue Imaging, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California 94720, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cell and Tissue Imaging, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California 94720, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"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":["Department of Computer Science, Old Dominion University, Norfolk, Virginia 23529, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, Virginia 23529, United States","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012671855","display_name":"Wade A. Hunter","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":"Wade Hunter","raw_affiliation_strings":["Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States","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":true,"raw_author_name":"Willy Wriggers","raw_affiliation_strings":["Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States"],"raw_orcid":"https://orcid.org/0000-0001-5326-3152","affiliations":[{"raw_affiliation_string":"Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States","institution_ids":["https://openalex.org/I81365321"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5010993930"],"corresponding_institution_ids":["https://openalex.org/I81365321"],"apc_list":null,"apc_paid":null,"fwci":1.2926,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.8480502,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"60","issue":"5","first_page":"2626","last_page":"2633"},"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":0.9987000226974487,"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":0.9987000226974487,"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/T11897","display_name":"Digital Holography and Microscopy","score":0.9923999905586243,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10572","display_name":"Geophysical and Geoelectrical Methods","score":0.9865000247955322,"subfield":{"id":"https://openalex.org/subfields/1908","display_name":"Geophysics"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/deconvolution","display_name":"Deconvolution","score":0.7515276670455933},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5946489572525024},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.588783860206604},{"id":"https://openalex.org/keywords/wedge","display_name":"Wedge (geometry)","score":0.5884580016136169},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.5203956365585327},{"id":"https://openalex.org/keywords/tomography","display_name":"Tomography","score":0.48982855677604675},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.484135240316391},{"id":"https://openalex.org/keywords/noise-reduction","display_name":"Noise reduction","score":0.41839033365249634},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.4178738296031952},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4036143720149994},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3372979760169983},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23063397407531738},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.19131219387054443},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.16561880707740784},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.13908889889717102},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.09833583235740662}],"concepts":[{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.7515276670455933},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5946489572525024},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.588783860206604},{"id":"https://openalex.org/C47422493","wikidata":"https://www.wikidata.org/wiki/Q2755127","display_name":"Wedge (geometry)","level":2,"score":0.5884580016136169},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.5203956365585327},{"id":"https://openalex.org/C163716698","wikidata":"https://www.wikidata.org/wiki/Q841267","display_name":"Tomography","level":2,"score":0.48982855677604675},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.484135240316391},{"id":"https://openalex.org/C163294075","wikidata":"https://www.wikidata.org/wiki/Q581861","display_name":"Noise reduction","level":2,"score":0.41839033365249634},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.4178738296031952},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4036143720149994},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3372979760169983},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23063397407531738},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.19131219387054443},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.16561880707740784},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13908889889717102},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.09833583235740662}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055032","descriptor_name":"Electron Microscope Tomography","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055032","descriptor_name":"Electron Microscope Tomography","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055032","descriptor_name":"Electron Microscope Tomography","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.9b01111","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01111","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:32045242","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32045242","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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8279804","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8279804","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":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8279804","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8279804","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":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8","score":0.6499999761581421}],"awards":[{"id":"https://openalex.org/G5889901336","display_name":null,"funder_award_id":"P01-GM051487","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5933034863","display_name":null,"funder_award_id":"R01-GM062968","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7653831880","display_name":null,"funder_award_id":"DBI-1356621","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"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1970101292","https://openalex.org/W2001735605","https://openalex.org/W2011038859","https://openalex.org/W2020435927","https://openalex.org/W2066071816","https://openalex.org/W2075641906","https://openalex.org/W2079228567","https://openalex.org/W2082990534","https://openalex.org/W2089704642","https://openalex.org/W2123022596","https://openalex.org/W2297140690","https://openalex.org/W2308727303","https://openalex.org/W2797054660","https://openalex.org/W2951698262","https://openalex.org/W2999706190","https://openalex.org/W4242391437"],"related_works":["https://openalex.org/W3090782779","https://openalex.org/W4251527294","https://openalex.org/W4250106855","https://openalex.org/W2037261263","https://openalex.org/W4380150146","https://openalex.org/W3149087629","https://openalex.org/W3024870410","https://openalex.org/W2410652950","https://openalex.org/W4231036715","https://openalex.org/W2032074591"],"abstract_inverted_index":{"Cryo-electron":[0],"tomography":[1],"maps":[2],"often":[3],"exhibit":[4],"considerable":[5],"noise":[6],"and":[7,15,41,54,93,132],"anisotropic":[8],"resolution,":[9],"due":[10],"to":[11,102,116],"the":[12,16,74,81,105,109,114,128],"low-dose":[13],"requirements":[14],"missing":[17,110],"wedge":[18],"in":[19,58,80,108],"Fourier":[20],"space.":[21],"These":[22],"spurious":[23],"features":[24],"are":[25,125],"visually":[26],"unappealing":[27],"and,":[28],"more":[29],"importantly,":[30],"prevent":[31],"an":[32],"automated":[33],"segmentation":[34],"of":[35,62,83,96,118,121,130],"geometric":[36],"shapes,":[37],"requiring":[38],"a":[39,47,69,91,94],"subjective":[40],"labor-intensive":[42],"manual":[43],"tracing.":[44],"We":[45,112],"developed":[46],"novel":[48],"computational":[49],"strategy":[50],"for":[51,104,127,144],"objectively":[52],"denoising":[53],"correcting":[55],"missing-wedge":[56],"artifacts":[57],"homogeneous":[59],"specimen":[60],"areas":[61],"tomograms,":[63],"where":[64],"it":[65],"is":[66],"assumed":[67],"that":[68,138],"template":[70,92,98],"repeats":[71],"itself":[72],"across":[73],"volume":[75],"under":[76],"consideration,":[77],"as":[78],"happens":[79],"case":[82],"filaments.":[84],"In":[85,134],"our":[86,139],"deconvolution":[87],"approach,":[88],"we":[89,136],"use":[90],"map":[95],"corresponding":[97],"locations,":[99],"allowing":[100],"us":[101],"compensate":[103],"information":[106],"lost":[107],"wedge.":[111],"applied":[113],"method":[115,140],"tomograms":[117],"actin-filament":[119],"bundles":[120],"inner-ear":[122],"stereocilia,":[123],"which":[124],"critical":[126],"senses":[129],"hearing":[131],"balance.":[133],"addition,":[135],"demonstrate":[137],"can":[141],"be":[142],"used":[143],"cell":[145],"membrane":[146],"detection.":[147]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
