{"id":"https://openalex.org/W6892945960","doi":"https://doi.org/10.5281/zenodo.12626122","title":"Data from: Denoising, Deblurring, and optical Deconvolution for cryo-ET and light microscopy with a physics-informed deep neural network DeBCR","display_name":"Data from: Denoising, Deblurring, and optical Deconvolution for cryo-ET and light microscopy with a physics-informed deep neural network DeBCR","publication_year":2024,"publication_date":"2024-07-03","ids":{"openalex":"https://openalex.org/W6892945960","doi":"https://doi.org/10.5281/zenodo.12626122"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.12626122","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.12626122","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"dataset"},"type":"dataset","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.12626122","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Li, Rui","orcid":"https://orcid.org/0000-0002-3085-5267"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]},{"id":"https://openalex.org/I2801798921","display_name":"Helmholtz-Zentrum Dresden-Rossendorf","ror":"https://ror.org/01zy2cs03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I2801798921"]},{"id":"https://openalex.org/I4210133756","display_name":"Center for Advanced Systems Understanding","ror":"https://ror.org/042b69396","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I2801798921","https://openalex.org/I4210133756"]},{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Li, Rui","raw_affiliation_strings":["Center for Advanced Systems Understanding","Helmholtz-Zentrum Dresden-Rossendorf","TU Dresden","Max Delbr\u00fcck Center for Molecular Medicine"],"raw_orcid":"https://orcid.org/0000-0002-3085-5267","affiliations":[{"raw_affiliation_string":"Center for Advanced Systems Understanding","institution_ids":["https://openalex.org/I4210133756"]},{"raw_affiliation_string":"Helmholtz-Zentrum Dresden-Rossendorf","institution_ids":["https://openalex.org/I2801798921"]},{"raw_affiliation_string":"TU Dresden","institution_ids":["https://openalex.org/I78650965"]},{"raw_affiliation_string":"Max Delbr\u00fcck Center for Molecular Medicine","institution_ids":["https://openalex.org/I205582932"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yushkevich, Artsemi","orcid":"https://orcid.org/0000-0002-8729-9281"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]},{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Yushkevich, Artsemi","raw_affiliation_strings":["Max Delbr\u00fcck Center for Molecular Medicine","Humboldt-Universit\u00e4t zu Berlin"],"raw_orcid":"https://orcid.org/0000-0002-8729-9281","affiliations":[{"raw_affiliation_string":"Max Delbr\u00fcck Center for Molecular Medicine","institution_ids":["https://openalex.org/I205582932"]},{"raw_affiliation_string":"Humboldt-Universit\u00e4t zu Berlin","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Chu, Xiaofeng","orcid":"https://orcid.org/0000-0001-6801-3949"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Chu, Xiaofeng","raw_affiliation_strings":["Max Delbr\u00fcck Center for Molecular Medicine","Charit\u00e9 - Universit\u00e4tsmedizin Berlin"],"raw_orcid":"https://orcid.org/0000-0001-6801-3949","affiliations":[{"raw_affiliation_string":"Max Delbr\u00fcck Center for Molecular Medicine","institution_ids":["https://openalex.org/I205582932"]},{"raw_affiliation_string":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","institution_ids":["https://openalex.org/I7877124"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Kudryashev, Mikhail","orcid":"https://orcid.org/0000-0003-3550-6274"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Kudryashev, Mikhail","raw_affiliation_strings":["Max Delbr\u00fcck Center for Molecular Medicine","Charit\u00e9 - Universit\u00e4tsmedizin Berlin"],"raw_orcid":"https://orcid.org/0000-0003-3550-6274","affiliations":[{"raw_affiliation_string":"Max Delbr\u00fcck Center for Molecular Medicine","institution_ids":["https://openalex.org/I205582932"]},{"raw_affiliation_string":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","institution_ids":["https://openalex.org/I7877124"]}]},{"author_position":"last","author":{"id":null,"display_name":"Yakimovich, Artur","orcid":"https://orcid.org/0000-0003-2458-4904"},"institutions":[{"id":"https://openalex.org/I219388962","display_name":"University of Wroc\u0142aw","ror":"https://ror.org/00yae6e25","country_code":"PL","type":"education","lineage":["https://openalex.org/I219388962"]},{"id":"https://openalex.org/I2801798921","display_name":"Helmholtz-Zentrum Dresden-Rossendorf","ror":"https://ror.org/01zy2cs03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I2801798921"]},{"id":"https://openalex.org/I4210133756","display_name":"Center for Advanced Systems Understanding","ror":"https://ror.org/042b69396","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I2801798921","https://openalex.org/I4210133756"]}],"countries":["DE","PL"],"is_corresponding":false,"raw_author_name":"Yakimovich, Artur","raw_affiliation_strings":["Center for Advanced Systems Understanding","Helmholtz-Zentrum Dresden-Rossendorf","University of Wroc\u0142aw"],"raw_orcid":"https://orcid.org/0000-0003-2458-4904","affiliations":[{"raw_affiliation_string":"Center for Advanced Systems Understanding","institution_ids":["https://openalex.org/I4210133756"]},{"raw_affiliation_string":"Helmholtz-Zentrum Dresden-Rossendorf","institution_ids":["https://openalex.org/I2801798921"]},{"raw_affiliation_string":"University of Wroc\u0142aw","institution_ids":["https://openalex.org/I219388962"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I205582932","https://openalex.org/I2801798921","https://openalex.org/I4210133756","https://openalex.org/I78650965"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/deconvolution","display_name":"Deconvolution","score":0.8528000116348267},{"id":"https://openalex.org/keywords/microscopy","display_name":"Microscopy","score":0.6640999913215637},{"id":"https://openalex.org/keywords/deblurring","display_name":"Deblurring","score":0.4903999865055084},{"id":"https://openalex.org/keywords/confocal-microscopy","display_name":"Confocal microscopy","score":0.475600004196167},{"id":"https://openalex.org/keywords/noise-reduction","display_name":"Noise reduction","score":0.43320000171661377},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.3734000027179718},{"id":"https://openalex.org/keywords/optical-microscope","display_name":"Optical microscope","score":0.36500000953674316},{"id":"https://openalex.org/keywords/fluorescence-microscope","display_name":"Fluorescence microscope","score":0.35089999437332153}],"concepts":[{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.8528000116348267},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.6640999913215637},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5755000114440918},{"id":"https://openalex.org/C2777693668","wikidata":"https://www.wikidata.org/wiki/Q25053743","display_name":"Deblurring","level":5,"score":0.4903999865055084},{"id":"https://openalex.org/C2779178360","wikidata":"https://www.wikidata.org/wiki/Q902045","display_name":"Confocal microscopy","level":2,"score":0.475600004196167},{"id":"https://openalex.org/C163294075","wikidata":"https://www.wikidata.org/wiki/Q581861","display_name":"Noise reduction","level":2,"score":0.43320000171661377},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4262999892234802},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.42399999499320984},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3734000027179718},{"id":"https://openalex.org/C77017923","wikidata":"https://www.wikidata.org/wiki/Q912313","display_name":"Optical microscope","level":3,"score":0.36500000953674316},{"id":"https://openalex.org/C169274487","wikidata":"https://www.wikidata.org/wiki/Q840211","display_name":"Fluorescence microscope","level":3,"score":0.35089999437332153},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.34950000047683716},{"id":"https://openalex.org/C113976765","wikidata":"https://www.wikidata.org/wiki/Q1823502","display_name":"Light sheet fluorescence microscopy","level":4,"score":0.3434999883174896},{"id":"https://openalex.org/C136009344","wikidata":"https://www.wikidata.org/wiki/Q336201","display_name":"Confocal","level":2,"score":0.32019999623298645},{"id":"https://openalex.org/C67649825","wikidata":"https://www.wikidata.org/wiki/Q196538","display_name":"Microscope","level":2,"score":0.31610000133514404},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.30959999561309814},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.3041999936103821},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.2987000048160553},{"id":"https://openalex.org/C62649853","wikidata":"https://www.wikidata.org/wiki/Q199687","display_name":"Remote sensing","level":1,"score":0.2867000102996826},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2856000065803528},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.2578999996185303},{"id":"https://openalex.org/C32277403","wikidata":"https://www.wikidata.org/wiki/Q740445","display_name":"Ridge","level":2,"score":0.25429999828338623},{"id":"https://openalex.org/C64297162","wikidata":"https://www.wikidata.org/wiki/Q1987070","display_name":"Deposition (geology)","level":3,"score":0.25369998812675476},{"id":"https://openalex.org/C55020928","wikidata":"https://www.wikidata.org/wiki/Q3813865","display_name":"Image quality","level":3,"score":0.25200000405311584}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5281/zenodo.12626122","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.12626122","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"dataset"}],"best_oa_location":{"id":"doi:10.5281/zenodo.12626122","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.12626122","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"dataset"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.4251885712146759,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Datasets":[0],"deposition":[1,147,167],"for":[2,9],"a":[3],"physics-informed":[4],"deep":[5],"learning":[6],"model":[7,21],"DeBCR":[8,20,48],"microscopy":[10,39,43,89,122],"image":[11,51],"restorations.":[12],"Leveraging":[13],"optics-based":[14],"physical":[15],"models":[16],"as":[17,63],"its":[18],"foundation,":[19],"demonstrates":[22],"superior":[23],"performance":[24],"in":[25],"denoising,":[26],"optical":[27],"deconvolution,":[28],"and":[29,41,61,223,230],"more":[30],"general":[31],"deblurring":[32],"(super-resolution,":[33],"SR)":[34],"tasks":[35],"across":[36],"both":[37],"light":[38],"(LM)":[40],"cryo-electron":[42],"(EM)":[44],"modalities.":[45],"To":[46],"evaluate":[47],"on":[49],"various":[50],"restoration":[52],"tasks,":[53],"several":[54],"previously":[55],"published":[56],"datasets":[57],"were":[58],"assembled,":[59],"pre-processed":[60],"provided":[62],"the":[64,81,114,146,166,188,213],"following:":[65],"LM:":[66,99,132,153],"2D":[67],"denoising":[68,101,176,199],"(files:":[69,102,137,158,177,200],"LM_2D_CARE_*.npz)":[70],"-":[71,104,139,160,179,202],"low/high":[72,105],"exposure":[73,106],"confocal":[74,107,154],"dataset":[75,108,141,162,181,204],"of":[76,83,109,116,142,163,182,205],"Schmidtea":[77],"mediterranea":[78],"(Denoising_Planaria)":[79],"from":[80,113,145,165,187,212],"publication":[82,115,190,214],"CARE":[84,117],"network":[85,118],"applied":[86,119],"to":[87,120],"fluorescent":[88,121],"data":[90,123,134,155],"(Weigert,":[91,124],"Schmidt,":[92,125],"Boothe":[93,126],"et":[94,127,192,218],"al.,":[95,128,193,219],"Nature":[96,129],"Methods,":[97,130],"2018).":[98,131],"3D":[100],"LM_3D_CARE_*.npz)":[103],"Tribolium":[110],"castaneum":[111],"(Denoising_Triboleum)":[112],"wide-field":[133],"deconvolution":[135,156],"(SR)":[136,157],"WF_SIM_S.aureus_*.npz)":[138],"widefield/SIM":[140],"Staphylococcus":[143],"aureus":[144],"(Pereira":[148],"&":[149,170],"Pinho,":[150],"Zenodo,":[151,172],"2021).":[152],"CF_STED_FActin_*.npz)":[159],"confocal/STED":[161],"F-actin":[164],"(Bouchard,":[168],"Gagn\u00e9":[169],"Lavoie-Cardinal,":[171],"2023).":[173],"EM:":[174,197],"low-frequency":[175],"EM_low_Tomo110_*.npz)":[178],"cryoET":[180,203],"Chlamydomonas":[183],"reinhardtii":[184],"cilia":[185],"(Tomo110)":[186],"cryo-CARE":[189],"(Buchholz":[191],"IEEE":[194],"(ISBI),":[195],"2019).":[196],"high-frequency":[198],"EM_high_RyR1_*.npz)":[201],"native":[206],"vesicles-embedded":[207],"membrane":[208],"protein":[209],"RyR1":[210],"(EMPIAR-10452)":[211],"(Sanchez,":[215],"Zhang,":[216],"Chen":[217],"Nat":[220],"Commun,":[221],"2020).":[222],"each":[224],"include":[225],"train":[226],"(*_train.npz),":[227],"test":[228],"(*_test.npz),":[229],"validation":[231],"(*_val.npz)":[232],"parts.":[233]},"counts_by_year":[],"updated_date":"2025-11-06T06:51:31.235846","created_date":"2025-10-10T00:00:00"}
