{"id":"https://openalex.org/W2063983719","doi":"https://doi.org/10.1186/1471-2105-10-178","title":"TOMOBFLOW: feature-preserving noise filtering for electron tomography","display_name":"TOMOBFLOW: feature-preserving noise filtering for electron tomography","publication_year":2009,"publication_date":"2009-06-12","ids":{"openalex":"https://openalex.org/W2063983719","doi":"https://doi.org/10.1186/1471-2105-10-178","mag":"2063983719"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-178","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-178","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-178","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-178","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044231334","display_name":"Jos\u00e9\u2010Jes\u00fas Fern\u00e1ndez","orcid":"https://orcid.org/0000-0003-2222-3355"},"institutions":[{"id":"https://openalex.org/I52354020","display_name":"University of Almer\u00eda","ror":"https://ror.org/003d3xx08","country_code":"ES","type":"education","lineage":["https://openalex.org/I52354020"]},{"id":"https://openalex.org/I4210104776","display_name":"Centro Nacional de Biotecnolog\u00eda","ror":"https://ror.org/015w4v032","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210104776"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Jose-Jesus Fernandez","raw_affiliation_strings":["Centro Nacional de Biotecnologia \u2013 CSIC, Campus de Cantoblanco, 28049, Madrid, Spain","Dept. Computer Architecture and Electronics, University of Almer\u00eda, 04120, Almer\u00eda, Spain"],"affiliations":[{"raw_affiliation_string":"Centro Nacional de Biotecnologia \u2013 CSIC, Campus de Cantoblanco, 28049, Madrid, Spain","institution_ids":["https://openalex.org/I4210104776"]},{"raw_affiliation_string":"Dept. Computer Architecture and Electronics, University of Almer\u00eda, 04120, Almer\u00eda, Spain","institution_ids":["https://openalex.org/I52354020"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5044231334"],"corresponding_institution_ids":["https://openalex.org/I4210104776","https://openalex.org/I52354020"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":4.7298,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.93679189,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"1","first_page":null,"last_page":null},"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":0.9983999729156494,"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":0.9983999729156494,"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":0.9911999702453613,"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":0.9657999873161316,"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/computer-science","display_name":"Computer science","score":0.7310501337051392},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.7084068655967712},{"id":"https://openalex.org/keywords/smoothing","display_name":"Smoothing","score":0.6861433386802673},{"id":"https://openalex.org/keywords/noise-reduction","display_name":"Noise reduction","score":0.6080684661865234},{"id":"https://openalex.org/keywords/anisotropic-diffusion","display_name":"Anisotropic diffusion","score":0.5841993689537048},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.49654489755630493},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.49578580260276794},{"id":"https://openalex.org/keywords/edge-preserving-smoothing","display_name":"Edge-preserving smoothing","score":0.49407508969306946},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.4649431109428406},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.42651379108428955},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.42392656207084656},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3408360481262207},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.29510393738746643},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07108402252197266}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7310501337051392},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.7084068655967712},{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.6861433386802673},{"id":"https://openalex.org/C163294075","wikidata":"https://www.wikidata.org/wiki/Q581861","display_name":"Noise reduction","level":2,"score":0.6080684661865234},{"id":"https://openalex.org/C203504353","wikidata":"https://www.wikidata.org/wiki/Q4765461","display_name":"Anisotropic diffusion","level":3,"score":0.5841993689537048},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.49654489755630493},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49578580260276794},{"id":"https://openalex.org/C141651230","wikidata":"https://www.wikidata.org/wiki/Q5337637","display_name":"Edge-preserving smoothing","level":4,"score":0.49407508969306946},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.4649431109428406},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.42651379108428955},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.42392656207084656},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3408360481262207},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.29510393738746643},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07108402252197266},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-10-178","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-178","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-178","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:digital.csic.es:10261/13970","is_oa":false,"landing_page_url":"http://hdl.handle.net/10261/13970","pdf_url":null,"source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"art\u00edculo"},{"id":"pmh:oai:doaj.org/article:d5f54136fcd64307951008463804dafd","is_oa":true,"landing_page_url":"https://doaj.org/article/d5f54136fcd64307951008463804dafd","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss 1, p 178 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2753846","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2753846","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-178","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-178","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-178","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2063983719.pdf","grobid_xml":"https://content.openalex.org/works/W2063983719.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W30830601","https://openalex.org/W107968503","https://openalex.org/W127809959","https://openalex.org/W1480546554","https://openalex.org/W1491716407","https://openalex.org/W1525153489","https://openalex.org/W1527543056","https://openalex.org/W1530741631","https://openalex.org/W1571699948","https://openalex.org/W1604713470","https://openalex.org/W1966786995","https://openalex.org/W1974531375","https://openalex.org/W1982459085","https://openalex.org/W1983923266","https://openalex.org/W1993161289","https://openalex.org/W1996586859","https://openalex.org/W1999619602","https://openalex.org/W2015876010","https://openalex.org/W2017451354","https://openalex.org/W2020221684","https://openalex.org/W2023119286","https://openalex.org/W2032146255","https://openalex.org/W2041956393","https://openalex.org/W2042049737","https://openalex.org/W2042243302","https://openalex.org/W2067987159","https://openalex.org/W2073985768","https://openalex.org/W2079123529","https://openalex.org/W2083019919","https://openalex.org/W2095132022","https://openalex.org/W2100702845","https://openalex.org/W2119988228","https://openalex.org/W2123176293","https://openalex.org/W2123902082","https://openalex.org/W2125419134","https://openalex.org/W2149112383","https://openalex.org/W2150134853","https://openalex.org/W2150876784","https://openalex.org/W2153261638","https://openalex.org/W2155186111","https://openalex.org/W2159907419","https://openalex.org/W2168896212","https://openalex.org/W2923753617","https://openalex.org/W4206519171","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2355942042","https://openalex.org/W2028472587","https://openalex.org/W1486519939","https://openalex.org/W2363077455","https://openalex.org/W2189489016","https://openalex.org/W2092056128","https://openalex.org/W2320510678","https://openalex.org/W2094277617","https://openalex.org/W2348951305","https://openalex.org/W3150714134"],"abstract_inverted_index":{"Noise":[0],"filtering":[1,17,45,78,98,135,143,179],"techniques":[2,18,46,57],"are":[3,19,58,62],"needed":[4],"in":[5,160,169,173],"electron":[6,167],"tomography":[7,168],"to":[8,64,67,109,128,151,162],"allow":[9,47],"proper":[10],"interpretation":[11],"of":[12,27,33,36,53,81,83,92,105,141,158,180,185,188],"datasets.":[13],"The":[14,117],"standard":[15],"linear":[16],"characterized":[20],"by":[21],"a":[22,74,96,133],"tradeoff":[23],"between":[24],"the":[25,31,34,39,68,93,103,106,139,186,204],"amount":[26],"reduced":[28],"noise":[29,48,77,178],"and":[30,61,156,171,198],"blurring":[32],"features":[35,187],"interest.":[37],"On":[38],"other":[40],"hand,":[41],"sophisticated":[42],"anisotropic":[43],"nonlinear":[44,97],"reduction":[49],"with":[50,79,138,149,153,183],"good":[51],"preservation":[52,82,184],"structures.":[54],"However,":[55],"these":[56],"computationally":[59],"intensive":[60],"difficult":[63],"be":[65,129],"tuned":[66,130],"problem":[69],"at":[70,203],"hand.":[71],"TOMOBFLOW":[72,132,146,175],"is":[73,88,147,201],"program":[75,136],"for":[76,166,195],"capabilities":[80],"biologically":[84],"relevant":[85],"information.":[86],"It":[87,200],"an":[89,110],"efficient":[90,177],"implementation":[91],"Beltrami":[94],"flow,":[95],"method":[99,121],"that":[100,119],"locally":[101],"tunes":[102],"strength":[104],"smoothing":[107],"according":[108],"edge":[111],"indicator":[112],"based":[113],"on":[114],"geometry":[115],"properties.":[116],"fact":[118],"this":[120],"does":[122],"not":[123],"have":[124],"free":[125],"parameters":[126],"hard":[127],"makes":[131],"user-friendly":[134],"equipped":[137],"power":[140],"diffusion-based":[142],"methods.":[144],"Furthermore,":[145],"provided":[148],"abilities":[150],"deal":[152],"different":[154],"types":[155],"formats":[157],"images":[159],"order":[161],"make":[163],"it":[164],"useful":[165],"particular":[170],"bioimaging":[172,181],"general.":[174],"allows":[176],"datasets":[182],"interest,":[189],"thereby":[190],"yielding":[191],"data":[192],"better":[193],"suited":[194],"post-processing,":[196],"visualization":[197],"interpretation.":[199],"available":[202],"web":[205],"site":[206],"http://www.ual.es/%7ejjfdez/SW/tomobflow.html":[207],".":[208]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":5}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2016-06-24T00:00:00"}
