https://m2.mtmt.hu/ eng 2026-10-24 23:02 JournalArticle 3148943 APPROVED true Funding Agency and Grant Number: recurrent Aix-Marseille Universite; CNRS; French-Hungarian international ANR Grant MULTISCALEFUNIM; ANR Grant BALAV1; FRM postdoctoral fellowship [SPF20130526842, ANR-13-NEUC-0005-01]; [SH/7/2/8]; [KMR_0214]; [FP7-ICT-2011-C 323945]; [KTIA_NAP_12-2-2015-0006]; Agence Nationale de la Recherche (ANR) [ANR-13-NEUC-0005] Funding Source: Agence Nationale de la Recherche (ANR) Funding text: We thank T.-W. Chen, K. Svoboda and the GENIE project at Janelia Research Campus for sharing their published GCaMP5 (ref. 15) and GCaMP6 (ref. 13) data, now available at http://crcns.org/, T.-W. Chen for sharing with us his ideas on the nonlinear modelling of GCaMP Ca2+ sensors and B. Bathellier, B. Kampa, G. Masson, K. Ocsai, T.-W. Chen and K. Svoboda for discussions and comments on the manuscript, K. Ocsai for help with programming and A. Meso for English editing. This work was supported by recurrent Aix-Marseille Universite and CNRS funding and by a French-Hungarian international ANR Grant MULTISCALEFUNIM to B.R. and I.V.; an ANR Grant BALAV1 to I.V.; SH/7/2/8, KMR_0214, FP7-ICT-2011-C 323945 and KTIA_NAP_12-2-2015-0006; A.K. has been funded by FRM postdoctoral fellowship SPF20130526842 and ANR-13-NEUC-0005-01. 0 2017-12-29T14:05:43.000+0000 false 3148943 2026-10-17T23:13:14.889+0000 2024-10-18T10:55:00.337+0000 2016-12-06T12:43:39.000+0000 true 10012926 Rózsa J. Balázs /api/author/10012926 Author true 10012926 2025-04-22T09:37:24.494+0000 2025-04-22T09:37:24.494+0000 true false true 24 24 /api/publicationtype/24 PublicationType 1 true 24 JournalArticle true 10000059 Article true 24 24 /api/publicationtype/24 PublicationType 1 true 24 JournalArticle /api/subtype/10000059 Szakcikk SubType 101 true 10000059 true 1 /api/category/1 Category true 1 Deneux, T Accurate spike estimation from noisy calcium signals for ultrafast three-dimensional imaging of large neuronal populations in vivo. true true /api/journal/10015678 REVIEWED true false 10015678 false 10015678 true 2041-1723 Journal FOREIGN 7 12190 12190 17 2016 Extracting neuronal spiking activity from large-scale two-photon recordings remains challenging, especially in mammals in vivo, where large noises often contaminate the signals. We propose a method, MLspike, which returns the most likely spike train underlying the measured calcium fluorescence. It relies on a physiological model including baseline fluctuations and distinct nonlinearities for synthetic and genetically encoded indicators. Model parameters can be either provided by the user or estimated from the data themselves. MLspike is computationally efficient thanks to its original discretization of probability representations; moreover, it can also return spike probabilities or samples. Benchmarked on extensive simulations and real data from seven different preparations, it outperformed state-of-the-art algorithms. Combined with the finding obtained from systematic data investigation (noise level, spiking rate and so on) that photonic noise is not necessarily the main limiting factor, our method allows spike extraction from large-scale recordings, as demonstrated on acousto-optical three-dimensional recordings of over 1,000 neurons in vivo. true true 2016 699456 true true true false true false GOLD 2026-10-18 true https://doi.org/10.1038/ncomms12190 true 10015544 Csajbók Edit /api/admin/10015544 Admin true 10015544 282 0 196 193 3 194 192 181 171 191 191 188 188 279 3 0 282 279 196 193 0 1 1 Folyóiratcikk Journal Article 24 175 Könyvrészlet Chapter in Book 25 20 Könyv Book 23 1 Egyéb konferenciaközlemény Conference paper 31 0 Egyéb konferenciakötet Conference proceedings 32 0 Oltalmi formák Protection forms 26 0 Disszertáció Thesis 28 40 Egyéb Miscellaneous 29 46 Alkotás Achievement 22 0 Kutatási adat Research data 33 0 Folyóiratcikk Journal Article 24 0 0 0 Könyvrészlet Chapter in Book 25 0 0 0 Könyv Book 23 0 0 0 Egyéb konferenciaközlemény Conference paper 31 0 0 0 Egyéb konferenciakötet Conference proceedings 32 0 0 0 Oltalmi formák Protection forms 26 0 0 0 Disszertáció Thesis 28 0 0 0 Egyéb Miscellaneous 29 0 0 0 Alkotás Achievement 22 0 0 0 Kutatási adat Research data 33 0 0 0 2015 0 1 1 1 1 2016 0 1 1 1 1 2017 0 16 15 16 15 2018 0 27 26 27 26 2019 0 29 28 29 28 2020 0 41 41 41 41 2021 0 33 33 33 33 2022 0 52 52 52 52 2023 0 25 25 25 25 2024 0 24 24 24 24 2025 0 22 22 22 22 2026 0 11 11 11 11 D1 A nemzetközi false 10054116,227,10012926 false false false 2017-12-29T14:05:43.000+0000 2016-12-06T12:44:58.000+0000 Információs Technológiai és Bionikai Kar (PPKE); MTA-PPKE ITK-NAP B Kétfoton méréstechnikai kuta... (PPKE / ITK); Neuronhálózat és Dendritikus Aktivitás Kutatócs... 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Balázs true 10012926 true Rozsa B true false false AuthorshipType 1 /api/authorshiptype/1 0 true 0 true false 25376723 true PersonAuthorship 8597031 /api/authorship/8597031 8 0.125 false true true Vanzetta I true false false AuthorshipType 1 /api/authorshiptype/1 0 true 0 true false 25376722 true PublicationIdentifier 1150995 /api/publicationidentifier/1150995 PlainSource 6 /api/publicationsource/6 PublicationSourceType 10001 /api/publicationsourcetype/10001 true true true DOI DOI https://doi.org/@@@ true true 6 true GOLD false IDENTICAL 10.1038/ncomms12190 https://doi.org/10.1038/ncomms12190 false 1501737 true PublicationIdentifier 1150993 /api/publicationidentifier/1150993 PlainSource 1 /api/publicationsource/1 PublicationSourceType 10003 /api/publicationsourcetype/10003 false true true WoS WoS https://www.webofscience.com/wos/woscc/full-record/@@@ true true 1 true false IDENTICAL 000380811100001 https://www.webofscience.com/wos/woscc/full-record/000380811100001 false 1534351 true PublicationIdentifier 1150994 /api/publicationidentifier/1150994 PlainSource 3 /api/publicationsource/3 PublicationSourceType 10003 /api/publicationsourcetype/10003 false true true Scopus Scopus http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-@@@ true true 3 true false IDENTICAL 84978946939 http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-84978946939 false 1534344 true PublicationIdentifier 1150996 /api/publicationidentifier/1150996 PlainSource 17 /api/publicationsource/17 PublicationSourceType 10003 /api/publicationsourcetype/10003 false true true PubMed PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=@@@&dopt=Abstract true true 17 true false IDENTICAL 27432255 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=27432255&dopt=Abstract false 1501738 true Classification 10154 /api/classification/10154 true true MtaRating 11551153 /api/mtarating/11551153 RatingType 10010 /api/ratingtype/10010 RegTB Institute 14100 /api/institute/14100 0 false true false Regionális Tudományok Bizottsága Committee on Regional Studies true 14100 true true true A nemzetközi true true SjrRating 10916864 /api/sjrrating/10916864 11 0.1 journal RatingType 10002 /api/ratingtype/10002 sjr true true ClassificationExternal 1301 /api/classificationexternal/1301 true 1301 true D1 DIRECT true true /api/publication/3148943 <div class="JournalArticle Publication long-list"> <div class="authors"> <img title="Forrásközlemény" style="float: left" src="/frontend/resources/grid/publication-core-icon.png"> <img title="Idézőközlemény" style="float: left" src="/frontend/resources/grid/publication-citation-icon.png"> <div class="autype autype0"> <span class="author-name" >Deneux T </span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" mtid="227"><a href="/gui2/?type=authors&mode=browse&sel=227" target="_blank">Kaszas A (<span class="authorship-author-name">Kaszás Attila</span> <span class="authorAux-mtmt"> Farmakológia</span>) </a> </span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" mtid="10054116"><a href="/gui2/?type=authors&mode=browse&sel=10054116" target="_blank">Szalay G (<span class="authorship-author-name">Szalay Gergely</span> <span class="authorAux-mtmt"> Idegtudomány</span>) </a> </span> <span class="author-affil"><span title="MTA Kísérleti Orvostudományi Kutatóintézet">IEMHAS</span>/<span title="Department of Pharmacology">DP</span>/Neuronhálózat és Dendritikus Aktivitás Kutatócsoport</span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" mtid="191"><a href="/gui2/?type=authors&mode=browse&sel=191" target="_blank">Katona G (<span class="authorship-author-name">Katona Gergely</span> <span class="authorAux-mtmt"> Farmakológia</span>) </a> </span> <span class="author-affil"><span title="Pázmány Péter Catholic University">PPCU</span>/<span title="Információs Technológiai és Bionikai Kar">ITK</span>/MTA-PPKE ITK-NAP B Two-photon measurement technology research group; <span title="MTA Kísérleti Orvostudományi Kutatóintézet">IEMHAS</span>/<span title="Department of Pharmacology">DP</span>/Neuronhálózat és Dendritikus Aktivitás Kutatócsoport</span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" >Lakner T </span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" >Grinvald A </span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" mtid="10012926"><a href="/gui2/?type=authors&mode=browse&sel=10012926" target="_blank">Rozsa B (<span class="authorship-author-name">Rózsa J. Balázs</span> <span class="authorAux-mtmt"> Idegtudomány, fizika</span>) </a> </span> <span class="author-affil"><span title="Pázmány Péter Catholic University">PPCU</span>/Információs Technológiai és Bionikai Kar; <span title="MTA Kísérleti Orvostudományi Kutatóintézet">IEMHAS</span>/<span title="Department of Pharmacology">DP</span>/Neuronhálózat és Dendritikus Aktivitás Kutatócsoport</span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" >Vanzetta I ✉ </span> </div> </div> <div class="title"><a href="/gui2/?mode=browse&params=publication;3148943" target="_blank">Accurate spike estimation from noisy calcium signals for ultrafast three-dimensional imaging of large neuronal populations in vivo.</a></div> <div> <span class="journal-title">NATURE COMMUNICATIONS</span> <span class="journal-issn">( <a target="_blank" href="https://portal.issn.org/resource/ISSN/2041-1723">2041-1723</a>)</span>: <span class="journal-volume">7</span> <span class="page"> Paper 12190. 17 p. </span> <span class="year">(2016)</span> </div> <div class="pub-footer"> <span class="language" xmlns="http://www.w3.org/1999/html">Language: English | </span> <span class="identifiers"> <span class="id identifier oa_GOLD" title=" Gold "> <a style="color:blue" title="10.1038/ncomms12190" target="_blank" href="https://doi.org/10.1038/ncomms12190"> DOI </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="000380811100001" target="_blank" href="https://www.webofscience.com/wos/woscc/full-record/000380811100001"> WoS </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="84978946939" target="_blank" href="http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-84978946939"> Scopus </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="27432255" target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=27432255&dopt=Abstract"> PubMed </a> </span> </span> <OnlyViewableByAuthor><div class="ratings"> <div class="journal-subject">Journal subject: Scopus - Biochemistry, Genetics and Molecular Biology (miscellaneous)&nbsp;&nbsp;&nbsp;Rank:&nbsp;D1</div> <div class="journal-subject">Journal subject: Scopus - Chemistry (miscellaneous)&nbsp;&nbsp;&nbsp;Rank:&nbsp;D1</div> <div class="journal-subject">Journal subject: Scopus - Physics and Astronomy (miscellaneous)&nbsp;&nbsp;&nbsp;Rank:&nbsp;D1</div> <div class="journal-subject">Committee on Regional Studies HASSELIX RTB [1901-]&nbsp;&nbsp;&nbsp;A nemzetközi</div> </div></OnlyViewableByAuthor> <div class="publication-citation" style="margin-left: 0.5cm;"> <span title="" class="citingPub-count">Citing papers: 282</span> | Independent citation: 279 | Self citation: 3 | Unknown citation: 0 | Number of citations in WoS: 181 | Number of citations in Scopus:&nbsp;171 | WoS/Scopus assigned:&nbsp;191 | Number of citations with DOI:&nbsp;192 </div> <div class="publication-citation"> <a target="_blank" href="/api/publication?cond=citations.related;eq;3148943&sort=publishedYear,desc&sort=title"> Number of cited publications: 1 </a> </div> <div class="mtid"><span class="long-pub-mtid">Publication: 3148943</span> | <span class="status-data status-APPROVED"> Published </span> <span class="oldId">Old id: 3148943</span> | Core Citing | <span class="type-subtype">Journal Article ( Article ) </span> | <span class="pub-category">Scientific</span> | <span class="publication-sourceOfData">MEDLINE</span> </div> <div class="lastModified">Last Modified: 2024.10.18. 12:55 Attila Kaszás (Farmakológia) </div> <pre class="comment" style="margin-top: 0; margin-bottom: 0;"><u>Comments</u>: Funding Agency and Grant Number: recurrent Aix-Marseille Universite; CNRS; French-Hungarian international ANR Grant MULTISCALEFUNIM; ANR Grant BALAV1; FRM postdoctoral fellowship [SPF20130526842, ANR-13-NEUC-0005-01]; [SH/7/2/8]; [KMR_0214]; [FP7-ICT-2011-C 323945]; [KTIA_NAP_12-2-2015-0006]; Agence Nationale de la Recherche (ANR) [ANR-13-NEUC-0005] Funding Source: Agence Nationale de la Re...</pre> </div></div>