{"id":"https://openalex.org/W3184729244","doi":"https://doi.org/10.1109/tci.2021.3097611","title":"Learning to Reconstruct Confocal Microscopy Stacks From Single Light Field Images","display_name":"Learning to Reconstruct Confocal Microscopy Stacks From Single Light Field Images","publication_year":2021,"publication_date":"2021-01-01","ids":{"openalex":"https://openalex.org/W3184729244","doi":"https://doi.org/10.1109/tci.2021.3097611","mag":"3184729244"},"language":"en","primary_location":{"id":"doi:10.1109/tci.2021.3097611","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tci.2021.3097611","pdf_url":null,"source":{"id":"https://openalex.org/S4210233665","display_name":"IEEE Transactions on Computational Imaging","issn_l":"2333-9403","issn":["2333-9403","2573-0436"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Imaging","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2003.11004.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007707727","display_name":"Josu\u00e9 Page Vizca\u00edno","orcid":"https://orcid.org/0000-0002-5848-3063"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Josu\u00e9 Page Vizca\u00edno","raw_affiliation_strings":["Department of Computer Science, University of Bern, Bern, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001201169","display_name":"Federico Saltarin","orcid":"https://orcid.org/0000-0002-4320-931X"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Federico Saltarin","raw_affiliation_strings":["Theodor Kocher Institute, University of Bern, Bern, Switzerland"],"affiliations":[{"raw_affiliation_string":"Theodor Kocher Institute, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041165358","display_name":"Yury Belyaev","orcid":"https://orcid.org/0000-0001-8318-2951"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Yury Belyaev","raw_affiliation_strings":["Microscopy Imaging Center, University of Bern, Bern, Switzerland"],"affiliations":[{"raw_affiliation_string":"Microscopy Imaging Center, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086503324","display_name":"Ruth Lyck","orcid":"https://orcid.org/0000-0002-6479-4837"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Ruth Lyck","raw_affiliation_strings":["Theodor Kocher Institute, University of Bern, Bern, Switzerland"],"affiliations":[{"raw_affiliation_string":"Theodor Kocher Institute, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021375348","display_name":"Tobias Lasser","orcid":"https://orcid.org/0000-0001-5669-920X"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tobias Lasser","raw_affiliation_strings":["Department of Informatics and Munich School of BioEngineering, Technical University of Munich, M&#x00FC;nchen, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Informatics and Munich School of BioEngineering, Technical University of Munich, M&#x00FC;nchen, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070940574","display_name":"Paolo Favaro","orcid":"https://orcid.org/0000-0003-3546-8247"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Paolo Favaro","raw_affiliation_strings":["Department of Informatics and Munich School of BioEngineering, Technical University of Munich, M&#x00FC;nchen, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Informatics and Munich School of BioEngineering, Technical University of Munich, M&#x00FC;nchen, Germany","institution_ids":["https://openalex.org/I62916508"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5007707727"],"corresponding_institution_ids":["https://openalex.org/I118564535"],"apc_list":null,"apc_paid":null,"fwci":7.2494,"has_fulltext":false,"cited_by_count":43,"citation_normalized_percentile":{"value":0.96801337,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"7","issue":null,"first_page":"775","last_page":"788"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9997000098228455,"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/T11569","display_name":"Optical Coherence Tomography Applications","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/confocal","display_name":"Confocal","score":0.739311933517456},{"id":"https://openalex.org/keywords/voxel","display_name":"Voxel","score":0.7113226056098938},{"id":"https://openalex.org/keywords/confocal-microscopy","display_name":"Confocal microscopy","score":0.7092750668525696},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.699256181716919},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6709930300712585},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6396912336349487},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.6207827925682068},{"id":"https://openalex.org/keywords/pixel","display_name":"Pixel","score":0.5983374118804932},{"id":"https://openalex.org/keywords/microscopy","display_name":"Microscopy","score":0.5106261372566223},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4747203588485718},{"id":"https://openalex.org/keywords/iterative-reconstruction","display_name":"Iterative reconstruction","score":0.45348235964775085},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.4276602566242218},{"id":"https://openalex.org/keywords/ground-truth","display_name":"Ground truth","score":0.411257266998291},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.34499621391296387},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.27413177490234375},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.22154060006141663}],"concepts":[{"id":"https://openalex.org/C136009344","wikidata":"https://www.wikidata.org/wiki/Q336201","display_name":"Confocal","level":2,"score":0.739311933517456},{"id":"https://openalex.org/C54170458","wikidata":"https://www.wikidata.org/wiki/Q663554","display_name":"Voxel","level":2,"score":0.7113226056098938},{"id":"https://openalex.org/C2779178360","wikidata":"https://www.wikidata.org/wiki/Q902045","display_name":"Confocal microscopy","level":2,"score":0.7092750668525696},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.699256181716919},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6709930300712585},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6396912336349487},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.6207827925682068},{"id":"https://openalex.org/C160633673","wikidata":"https://www.wikidata.org/wiki/Q355198","display_name":"Pixel","level":2,"score":0.5983374118804932},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.5106261372566223},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4747203588485718},{"id":"https://openalex.org/C141379421","wikidata":"https://www.wikidata.org/wiki/Q6094427","display_name":"Iterative reconstruction","level":2,"score":0.45348235964775085},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.4276602566242218},{"id":"https://openalex.org/C146849305","wikidata":"https://www.wikidata.org/wiki/Q370766","display_name":"Ground truth","level":2,"score":0.411257266998291},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.34499621391296387},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.27413177490234375},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.22154060006141663}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/tci.2021.3097611","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tci.2021.3097611","pdf_url":null,"source":{"id":"https://openalex.org/S4210233665","display_name":"IEEE Transactions on Computational Imaging","issn_l":"2333-9403","issn":["2333-9403","2573-0436"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Imaging","raw_type":"journal-article"},{"id":"mag:3013429942","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/2003.11004.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:oai:boris.unibe.ch:163638","is_oa":false,"landing_page_url":"https://boris.unibe.ch/163638/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401086","display_name":"Bern Open Repository and Information System (University of Bern)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I118564535","host_organization_name":"University of Bern","host_organization_lineage":["https://openalex.org/I118564535"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Vizcaino, Josue Page; Saltarin, Federico; Belyaev, Yury; Lyck, Ruth; Lasser, Tobias; Favaro, Paolo (2021). Learning to Reconstruct Confocal Microscopy Stacks From Single Light Field Images. IEEE transactions on computational imaging, 7, pp. 775-788. IEEE 10.1109/TCI.2021.3097611 &lt;http://dx.doi.org/10.1109/TCI.2021.3097611&gt;","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"mag:3013429942","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/2003.11004.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},"sustainable_development_goals":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"awards":[{"id":"https://openalex.org/G6087138287","display_name":null,"funder_award_id":"3264/2-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320310992","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":74,"referenced_works":["https://openalex.org/W1540070193","https://openalex.org/W1901129140","https://openalex.org/W1986142635","https://openalex.org/W1994574914","https://openalex.org/W2001674689","https://openalex.org/W2060167709","https://openalex.org/W2063094145","https://openalex.org/W2064843545","https://openalex.org/W2067422832","https://openalex.org/W2087309216","https://openalex.org/W2105198794","https://openalex.org/W2105787298","https://openalex.org/W2108598243","https://openalex.org/W2128268941","https://openalex.org/W2132537080","https://openalex.org/W2133515844","https://openalex.org/W2133665775","https://openalex.org/W2134091142","https://openalex.org/W2137313943","https://openalex.org/W2161196156","https://openalex.org/W2304648132","https://openalex.org/W2331128040","https://openalex.org/W2386621445","https://openalex.org/W2464708700","https://openalex.org/W2611648074","https://openalex.org/W2661720377","https://openalex.org/W2754636875","https://openalex.org/W2781310020","https://openalex.org/W2800089816","https://openalex.org/W2806336474","https://openalex.org/W2836171385","https://openalex.org/W2897864842","https://openalex.org/W2898972076","https://openalex.org/W2945201726","https://openalex.org/W2949493305","https://openalex.org/W2950291885","https://openalex.org/W2950754606","https://openalex.org/W2950775992","https://openalex.org/W2951706657","https://openalex.org/W2954117664","https://openalex.org/W2962914239","https://openalex.org/W2964054038","https://openalex.org/W2966800242","https://openalex.org/W2969578656","https://openalex.org/W2972808355","https://openalex.org/W2981006361","https://openalex.org/W2981517676","https://openalex.org/W2981963355","https://openalex.org/W2989433233","https://openalex.org/W2989882321","https://openalex.org/W2998660946","https://openalex.org/W3015700660","https://openalex.org/W3027482364","https://openalex.org/W3035479716","https://openalex.org/W3082328657","https://openalex.org/W3084022149","https://openalex.org/W3091938789","https://openalex.org/W3094118223","https://openalex.org/W3099844944","https://openalex.org/W3101351793","https://openalex.org/W3126189420","https://openalex.org/W3137540208","https://openalex.org/W3158688284","https://openalex.org/W3178685243","https://openalex.org/W4308067211","https://openalex.org/W6639824700","https://openalex.org/W6680045439","https://openalex.org/W6680152570","https://openalex.org/W6697974390","https://openalex.org/W6737286391","https://openalex.org/W6752212363","https://openalex.org/W6798264256","https://openalex.org/W6888449165","https://openalex.org/W7028878841"],"related_works":["https://openalex.org/W2726111829","https://openalex.org/W4250585504","https://openalex.org/W2008049857","https://openalex.org/W1978803831","https://openalex.org/W2105513520","https://openalex.org/W2580002495","https://openalex.org/W2056668469","https://openalex.org/W82035557","https://openalex.org/W4285171187","https://openalex.org/W1972388159"],"abstract_inverted_index":{"We":[0,153],"present":[1],"a":[2,24,48,63,175,186],"novel":[3],"deep":[4],"learning":[5],"approach":[6,102],"to":[7,42,79,147,170],"reconstruct":[8,43,171],"confocal":[9,46,80,206],"microscopy":[10],"stacks":[11],"from":[12],"single":[13,64],"light":[14,65,191],"field":[15,66,192],"images.":[16],"To":[17,94,180],"perform":[18],"the":[19,32,75,85,91,120,148,158,162,195,200],"reconstruction,":[20],"we":[21,184,209],"introduce":[22],"LFMNet,":[23],"fully":[25],"convolutional":[26],"neural":[27],"network":[28,163],"architecture":[29,164],"inspired":[30],"by":[31],"U-Net":[33],"design.":[34],"A":[35],"property":[36],"of":[37,68,82,119,157,161,166,189,194,204],"LFMNet":[38],"is":[39,103,151],"its":[40,96],"ability":[41],"with":[44,113],"near":[45],"accuracy":[47],"112":[49],"\u00d7112":[50],"\u00d757.6":[51],"\u03bcm":[52],"<sup":[53],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[54],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">3</sup>":[55],"volume":[56],"(1287\u00d71287\u00d764":[57],"voxels)":[58],"in":[59,98,123,141],"50":[60],"ms":[61],"given":[62,176],"image":[67,124],"1287\u00d71287":[69],"pixels,":[70],"thus":[71],"dramatically":[72],"reducing":[73],"720-fold":[74],"capture":[76],"time":[77,150],"compared":[78],"scanning":[81],"assays":[83],"at":[84],"same":[86],"volumetric":[87],"resolution":[88],"and":[89,107,129,137,140,165,199],"64-fold":[90],"required":[92],"storage.":[93],"prove":[95],"applicability":[97],"life":[99],"sciences,":[100],"our":[101,127,167,182],"evaluated":[104],"both":[105],"quantitatively":[106],"qualitatively":[108],"on":[109],"mouse":[110,196],"brain":[111,197],"slices":[112],"fluorescently":[114],"labeled":[115],"blood":[116],"vessels.":[117],"Because":[118],"drastic":[121],"reduction":[122],"acquisition":[125],"time,":[126],"setup":[128],"method":[130],"are":[131],"suitable":[132],"for":[133,174,221],"imaging":[134],"highly":[135],"dynamic":[136],"light-sensitive":[138],"events,":[139],"closed-loop":[142],"systems,":[143],"where":[144],"latency":[145],"due":[146],"reconstruction":[149],"crucial.":[152],"provide":[154],"empirical":[155],"analysis":[156],"optical":[159],"design,":[160],"training":[168],"procedure":[169],"confocal-like":[172],"volumes":[173],"target":[177],"depth":[178],"range.":[179],"train":[181],"network,":[183],"built":[185],"data":[187,215],"set":[188,203,216],"362":[190],"images":[193],"sample":[198],"corresponding":[201],"aligned":[202],"3D":[205],"scans,":[207],"which":[208],"use":[210],"as":[211],"ground":[212],"truth.":[213],"The":[214],"will":[217],"be":[218],"made":[219],"available":[220],"research":[222],"purposes.":[223]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
