{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T02:15:36Z","timestamp":1780366536155,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006157","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,6,12]],"date-time":"2018-06-12T00:00:00Z","timestamp":1528761600000}}],"reference-count":29,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2018,5,21]],"date-time":"2018-05-21T00:00:00Z","timestamp":1526860800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["01GQ1002"],"award-info":[{"award-number":["01GQ1002"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["01GQ1002"],"award-info":[{"award-number":["01GQ1002"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["01GQ1601"],"award-info":[{"award-number":["01GQ1601"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["EXC307"],"award-info":[{"award-number":["EXC307"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["BE5601\/1-1"],"award-info":[{"award-number":["BE5601\/1-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB 1233"],"award-info":[{"award-number":["SFB 1233"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB 1089"],"award-info":[{"award-number":["SFB 1089"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["108726"],"award-info":[{"award-number":["108726"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["95668"],"award-info":[{"award-number":["95668"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Wellcome Trust","award":["95669"],"award-info":[{"award-number":["95669"]}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["P300P2 158428"],"award-info":[{"award-number":["P300P2 158428"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001645","name":"Boehringer Ingelheim Fonds","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001645","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004784","name":"Novartis Stiftung f\u00fcr Medizinisch-Biologische Forschung","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004784","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Simmons Family Foundation (US)","award":["325171, 325398, 365002"],"award-info":[{"award-number":["325171, 325398, 365002"]}]},{"DOI":"10.13039\/100006754","name":"Army Research Laboratory","doi-asserted-by":"publisher","award":["W911NF-12-1-0594"],"award-info":[{"award-number":["W911NF-12-1-0594"]}],"id":[{"id":"10.13039\/100006754","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01EB22913, R21EY027592"],"award-info":[{"award-number":["R01EB22913, R21EY027592"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000185","name":"Defense Advanced Research Projects Agency","doi-asserted-by":"publisher","award":["N66001-15-C-4032, SIMPLEX"],"award-info":[{"award-number":["N66001-15-C-4032, SIMPLEX"]}],"id":[{"id":"10.13039\/100000185","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DP1 EY023176"],"award-info":[{"award-number":["DP1 EY023176"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011039","name":"Intelligence Advanced Research Projects Activity","doi-asserted-by":"publisher","award":["D16PC00003, D16PC0000"],"award-info":[{"award-number":["D16PC00003, D16PC0000"]}],"id":[{"id":"10.13039\/100011039","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["BE5601\/4-1"],"award-info":[{"award-number":["BE5601\/4-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006157","type":"journal-article","created":{"date-parts":[[2018,5,21]],"date-time":"2018-05-21T14:44:15Z","timestamp":1526913855000},"page":"e1006157","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":155,"title":["Community-based benchmarking improves spike rate inference from two-photon calcium imaging data"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0199-4727","authenticated-orcid":true,"given":"Philipp","family":"Berens","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy","family":"Freeman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9330-7655","authenticated-orcid":true,"given":"Thomas","family":"Deneux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikolay","family":"Chenkov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0027-0580","authenticated-orcid":true,"given":"Thomas","family":"McColgan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Artur","family":"Speiser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jakob H.","family":"Macke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3247-6487","authenticated-orcid":true,"given":"Srinivas C.","family":"Turaga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5519-842X","authenticated-orcid":true,"given":"Patrick","family":"Mineault","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8235-8257","authenticated-orcid":true,"given":"Peter","family":"Rupprecht","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4454-6171","authenticated-orcid":true,"given":"Stephan","family":"Gerhard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8803-2976","authenticated-orcid":true,"given":"Rainer W.","family":"Friedrich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1321-5866","authenticated-orcid":true,"given":"Johannes","family":"Friedrich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liam","family":"Paninski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7106-814X","authenticated-orcid":true,"given":"Marius","family":"Pachitariu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4922-3972","authenticated-orcid":true,"given":"Kenneth D.","family":"Harris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ben","family":"Bolte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy A.","family":"Machado","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dario","family":"Ringach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0690-0141","authenticated-orcid":true,"given":"Jasmine","family":"Stone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luke E.","family":"Rogerson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas J.","family":"Sofroniew","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob","family":"Reimer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3249-3845","authenticated-orcid":true,"given":"Emmanouil","family":"Froudarakis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4567-6966","authenticated-orcid":true,"given":"Thomas","family":"Euler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miroslav","family":"Rom\u00e1n Ros\u00f3n","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucas","family":"Theis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4305-6376","authenticated-orcid":true,"given":"Andreas S.","family":"Tolias","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias","family":"Bethge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,5,21]]},"reference":[{"issue":"3","key":"ref1","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/nrn2338","article-title":"Imaging in vivo: watching the brain in action","volume":"9","author":"JN Kerr","year":"2008","journal-title":"Nature Reviews Neuroscience"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.conb.2015.03.016","article-title":"Comprehensive imaging of cortical networks","volume":"32","author":"S Peron","year":"2015","journal-title":"Current Opinion in Neurobiology"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"151","DOI":"10.3389\/fncir.2013.00151","article-title":"Three-dimensional mapping of microcircuit correlation structure","volume":"7","author":"RJ Cotton","year":"2013","journal-title":"Frontiers in neural circuits"},{"issue":"5","key":"ref4","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/nmeth.1453","article-title":"High-speed in vivo calcium imaging reveals neuronal network activity with near-millisecond precision","volume":"7","author":"BF Grewe","year":"2010","journal-title":"Nature methods"},{"key":"ref5","article-title":"Robustness of spike deconvolution for calcium imaging of neural spiking","author":"M Pachitariu","year":"2017","journal-title":"bioRxiv"},{"issue":"2","key":"ref6","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1016\/j.bpj.2008.08.005","article-title":"Spike inference from calcium imaging using sequential Monte Carlo methods","volume":"97","author":"JT Vogelstein","year":"2009","journal-title":"Biophysical journal"},{"issue":"7458","key":"ref7","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1038\/nature12354","article-title":"Ultrasensitive fluorescent proteins for imaging neuronal activity","volume":"499","author":"TW Chen","year":"2013","journal-title":"Nature"},{"issue":"1","key":"ref8","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.bpj.2012.07.058","article-title":"Photon shot noise limits on optical detection of neuronal spikes and estimation of spike timing","volume":"104","author":"B Wilt","year":"2013","journal-title":"Biophysical journal"},{"issue":"6","key":"ref9","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1152\/jn.01073.2009","article-title":"Fast nonnegative deconvolution for spike train inference from population calcium imaging","volume":"104","author":"JT Vogelstein","year":"2010","journal-title":"Journal of neurophysiology"},{"issue":"5","key":"ref10","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/nmeth874","article-title":"Reconstruction of firing rate changes across neuronal populations by temporally deconvolved Ca 2+ imaging","volume":"3","author":"E Yaksi","year":"2006","journal-title":"Nature methods"},{"issue":"7","key":"ref11","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1038\/nn.2140","article-title":"Population imaging of ongoing neuronal activity in the visual cortex of awake rats","volume":"11","author":"DS Greenberg","year":"2008","journal-title":"Nature neuroscience"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"12190","DOI":"10.1038\/ncomms12190","article-title":"Accurate spike estimation from noisy calcium signals for ultrafast three-dimensional imaging of large neuronal populations in vivo","volume":"7","author":"T Deneux","year":"2016","journal-title":"Nature Communications"},{"issue":"3","key":"ref13","doi-asserted-by":"crossref","first-page":"e1005423","DOI":"10.1371\/journal.pcbi.1005423","article-title":"Fast online deconvolution of calcium imaging data","volume":"13","author":"J Friedrich","year":"2017","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"ref14","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1152\/jn.00084.2008","article-title":"Fast and accurate detection of action potentials from somatic calcium fluctuations","volume":"100","author":"T Sasaki","year":"2008","journal-title":"Journal of neurophysiology"},{"issue":"3","key":"ref15","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.neuron.2016.04.014","article-title":"Benchmarking Spike Rate Inference in Population Calcium Imaging","volume":"90","author":"L Theis","year":"2016","journal-title":"Neuron"},{"issue":"3","key":"ref16","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1007\/s11263-015-0816-y","article-title":"Imagenet large scale visual recognition challenge","volume":"115","author":"O Russakovsky","year":"2015","journal-title":"International Journal of Computer Vision"},{"key":"ref17","doi-asserted-by":"crossref","unstructured":"Adam-Bourdarios C, Cowan G, Germain C, Guyon I, K\u00e9gl B, Rousseau D. The Higgs boson machine learning challenge. In: NIPS 2014 Workshop on High-energy Physics and Machine Learning; 2015. p. 19\u201355.","DOI":"10.1088\/1742-6596\/664\/7\/072015"},{"key":"ref18","unstructured":"Svoboda K, Project G. Simultaneous imaging and loose-seal cell-attached electrical recordings from neurons expressing a variety of genetically encoded calcium indicators; 2015. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/dx.doi.org\/10.6080\/K02R3PMN\" xlink:type=\"simple\">http:\/\/dx.doi.org\/10.6080\/K02R3PMN<\/ext-link>."},{"key":"ref19","unstructured":"Friedrich J, Paninski L. Fast active set methods for online spike inference from calcium imaging. In: Advances In Neural Information Processing Systems; 2016. p. 1984\u20131992."},{"key":"ref20","doi-asserted-by":"crossref","unstructured":"He K, Zhang X, Ren S, Sun J. Deep residual learning for image recognition. In: Proceedings of the IEEE conference on computer vision and pattern recognition; 2016. p. 770\u2013778.","DOI":"10.1109\/CVPR.2016.90"},{"key":"ref21","doi-asserted-by":"crossref","unstructured":"Szegedy C, Liu W, Jia Y, Sermanet P, Reed S, Anguelov D, et al. Going deeper with convolutions. CVPR; 2015.","DOI":"10.1109\/CVPR.2015.7298594"},{"key":"ref22","unstructured":"Speiser A, Yan J, Archer E, Buesing L, Turaga SC, Macke JH. Fast amortized inference of neural activity from calcium imaging data with variational autoencoders. In: Advances in Neural Information Processing Systems. vol. 30; 2017."},{"issue":"52","key":"ref23","doi-asserted-by":"crossref","first-page":"16054","DOI":"10.1073\/pnas.1510393112","article-title":"Information-theoretic model comparison unifies saliency metrics","volume":"112","author":"M Kuemmerer","year":"2015","journal-title":"Proceedings of the National Academy of Science"},{"key":"ref24","doi-asserted-by":"crossref","unstructured":"K\u00fcmmerer M, Wallis TS, Bethge M. Saliency Benchmarking: Separating Models, Maps and Metrics. arXiv preprint arXiv:1704.08615. 2017.","DOI":"10.1007\/978-3-030-01270-0_47"},{"key":"ref25","article-title":"CosMIC: A Consistent Metric for Spike Inference from Calcium Imaging","author":"S Reynolds","year":"2017","journal-title":"bioRxiv"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.conb.2015.04.002","article-title":"Open source tools for large-scale neuroscience","volume":"32","author":"J Freeman","year":"2015","journal-title":"Current Opinion in Neurobiology"},{"issue":"2","key":"ref27","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.neuron.2015.11.037","article-title":"Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data","volume":"89","author":"EA Pnevmatikakis","year":"2016","journal-title":"Neuron"},{"key":"ref28","article-title":"Suite2p: beyond 10,000 neurons with standard two-photon microscopy","author":"M Pachitariu","year":"2016","journal-title":"bioRxiv"},{"key":"ref29","first-page":"2825","article-title":"Scikit-learn: Machine Learning in Python","volume":"12","author":"F Pedregosa","year":"2011","journal-title":"Journal of Machine Learning Research"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006157","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,6,12]],"date-time":"2018-06-12T00:00:00Z","timestamp":1528761600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006157","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,18]],"date-time":"2019-10-18T04:22:50Z","timestamp":1571372570000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006157"}},"subtitle":[],"editor":[{"given":"Daniel","family":"Bush","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,5,21]]},"references-count":29,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2018,5,21]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006157","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/177956","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,5,21]]}}}