{"id":"https://openalex.org/W2922203751","doi":"https://doi.org/10.1177/1094342019832958","title":"A GPU acceleration of 3-D Fourier reconstruction in cryo-EM","display_name":"A GPU acceleration of 3-D Fourier reconstruction in cryo-EM","publication_year":2019,"publication_date":"2019-03-11","ids":{"openalex":"https://openalex.org/W2922203751","doi":"https://doi.org/10.1177/1094342019832958","mag":"2922203751"},"language":"en","primary_location":{"id":"doi:10.1177/1094342019832958","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342019832958","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5068360342","display_name":"David St\u0159el\u00e1k","orcid":"https://orcid.org/0000-0003-4513-4718"},"institutions":[{"id":"https://openalex.org/I4210155092","display_name":"Czech Academy of Sciences, Institute of Computer Science","ror":"https://ror.org/0496n6574","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210155092"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"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":["CZ","ES"],"is_corresponding":false,"raw_author_name":"David St\u0159el\u00e1k","raw_affiliation_strings":["Institute of Computer Science, Masaryk University, Brno, Czech Republic","National Center for Biotechnology, Spanish National Research Council, Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261","https://openalex.org/I4210155092"]},{"raw_affiliation_string":"National Center for Biotechnology, Spanish National Research Council, Madrid, Spain","institution_ids":["https://openalex.org/I4210104776"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007117539","display_name":"Carlos \u00d3scar S. Sorzano","orcid":"https://orcid.org/0000-0002-9473-283X"},"institutions":[{"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":false,"raw_author_name":"Carlos \u00d3scar S Sorzano","raw_affiliation_strings":["National Center for Biotechnology, Spanish National Research Council, Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology, Spanish National Research Council, Madrid, Spain","institution_ids":["https://openalex.org/I4210104776"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046960969","display_name":"J.M. Carazo","orcid":"https://orcid.org/0000-0003-0788-8447"},"institutions":[{"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":false,"raw_author_name":"Jos\u00e9 Mar\u00eda Carazo","raw_affiliation_strings":["National Center for Biotechnology, Spanish National Research Council, Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology, Spanish National Research Council, Madrid, Spain","institution_ids":["https://openalex.org/I4210104776"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089216324","display_name":"Ji\u0159\u00ed Filipovi\u010d","orcid":"https://orcid.org/0000-0002-5703-9673"},"institutions":[{"id":"https://openalex.org/I4210155092","display_name":"Czech Academy of Sciences, Institute of Computer Science","ror":"https://ror.org/0496n6574","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210155092"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Ji\u0159\u00ed Filipovi\u010d","raw_affiliation_strings":["Institute of Computer Science, Masaryk University, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261","https://openalex.org/I4210155092"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5089216324"],"corresponding_institution_ids":["https://openalex.org/I21449261","https://openalex.org/I4210155092"],"apc_list":null,"apc_paid":null,"fwci":2.1001,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.90014265,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"33","issue":"5","first_page":"948","last_page":"959"},"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":0.9998999834060669,"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":0.9998999834060669,"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/T12039","display_name":"Electron and X-Ray Spectroscopy Techniques","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/2508","display_name":"Surfaces, Coatings and Films"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11183","display_name":"Advanced X-ray Imaging Techniques","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/3108","display_name":"Radiation"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.9219520092010498},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.7988139390945435},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7794725298881531},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6949597001075745},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.598414421081543},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.5803734064102173},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.5434021353721619},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5021665096282959},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.4875587821006775},{"id":"https://openalex.org/keywords/coprocessor","display_name":"Coprocessor","score":0.4622933566570282},{"id":"https://openalex.org/keywords/central-processing-unit","display_name":"Central processing unit","score":0.4481493830680847},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3762671947479248},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.2886039614677429},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.20737943053245544},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.1390565037727356},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08240768313407898}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.9219520092010498},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.7988139390945435},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7794725298881531},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6949597001075745},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.598414421081543},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.5803734064102173},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.5434021353721619},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5021665096282959},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.4875587821006775},{"id":"https://openalex.org/C86111242","wikidata":"https://www.wikidata.org/wiki/Q859595","display_name":"Coprocessor","level":2,"score":0.4622933566570282},{"id":"https://openalex.org/C49154492","wikidata":"https://www.wikidata.org/wiki/Q5300","display_name":"Central processing unit","level":2,"score":0.4481493830680847},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3762671947479248},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.2886039614677429},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.20737943053245544},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.1390565037727356},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08240768313407898},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1177/1094342019832958","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342019832958","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},{"id":"pmh:oai:digital.csic.es:10261/239852","is_oa":false,"landing_page_url":"http://hdl.handle.net/10261/239852","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"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6299999952316284,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G5466896682","display_name":null,"funder_award_id":"CZ.02.1.01/0.0/0.0/16_013/0001802","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"}],"funders":[{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W634494034","https://openalex.org/W1594672787","https://openalex.org/W1973838566","https://openalex.org/W2019087987","https://openalex.org/W2065129422","https://openalex.org/W2067374400","https://openalex.org/W2127581985","https://openalex.org/W2150703397","https://openalex.org/W2151073381","https://openalex.org/W2432427150","https://openalex.org/W2587625522","https://openalex.org/W2753970948","https://openalex.org/W2768520977","https://openalex.org/W4242391437"],"related_works":["https://openalex.org/W1963859303","https://openalex.org/W2364044215","https://openalex.org/W3145240193","https://openalex.org/W2389600408","https://openalex.org/W240129890","https://openalex.org/W3048701459","https://openalex.org/W2147073383","https://openalex.org/W2020279179","https://openalex.org/W1972148443","https://openalex.org/W2154903817"],"abstract_inverted_index":{"Cryo-electron":[0],"microscopy":[1],"is":[2,22,140],"a":[3,12,20,32,41,71,77,91,112,125,133,184],"popular":[4],"method":[5],"for":[6,48,64,124],"macromolecules":[7],"structure":[8],"determination.":[9],"Reconstruction":[10],"of":[11,28,53,74,85,117,127],"3-D":[13,60,107],"volume":[14,61],"from":[15,19],"raw":[16],"data":[17],"obtained":[18],"microscope":[21],"highly":[23],"computationally":[24],"demanding.":[25],"Thus,":[26],"acceleration":[27],"the":[29,54,59,83,86,106,154],"reconstruction":[30,62],"has":[31],"great":[33],"practical":[34],"value.":[35],"In":[36],"this":[37],"article,":[38],"we":[39,166],"introduce":[40,111],"novel":[42],"graphics":[43],"processing":[44],"unit":[45],"(GPU)-friendly":[46],"algorithm":[47,89],"direct":[49],"Fourier":[50],"reconstruction,":[51],"one":[52],"main":[55],"computational":[56],"bottlenecks":[57],"in":[58,102,142],"pipeline":[63],"some":[65],"experimental":[66],"cases":[67],"(particularly":[68],"those":[69],"with":[70,161],"large":[72],"number":[73],"images":[75],"and":[76,98,174],"high":[78],"internal":[79],"symmetry).":[80],"Contrary":[81],"to":[82,122,153,178],"state":[84],"art,":[87],"our":[88,118],"uses":[90],"gather":[92],"memory":[93,186],"pattern,":[94],"improving":[95],"cache":[96],"locality":[97],"removing":[99],"race":[100],"conditions":[101],"parallel":[103,156],"writing":[104],"into":[105],"volume.":[108],"We":[109],"also":[110],"finely":[113],"tuned":[114],"CUDA":[115,138],"implementation":[116,139,158,181],"algorithm,":[119],"using":[120,159,171],"auto-tuning":[121],"search":[123],"combination":[126],"optimization":[128],"parameters":[129],"maximizing":[130],"performance":[131],"on":[132,183],"given":[134],"GPU":[135,160,180],"architecture.":[136],"Our":[137],"integrated":[141],"widely":[143],"used":[144],"software":[145],"Xmipp,":[146],"version":[147],"3.19,":[148],"reaching":[149],"11.4\u00d7":[150],"speedup":[151,170,176],"compared":[152,177],"original":[155],"CPU":[157],"comparable":[162],"power":[163],"consumption.":[164],"Moreover,":[165],"have":[167],"reached":[168],"31.7\u00d7":[169],"four":[172],"GPUs":[173],"2.14\u00d7\u20135.96\u00d7":[175],"optimized":[179],"based":[182],"scatter":[185],"pattern.":[187]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
