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activity","volume":"499","author":"TW Chen","year":"2013","journal-title":"Nature"},{"key":"ref24","unstructured":"GENIE project, Janelia Research Campus, HHMI; Karel Svoboda (contact). Simultaneous imaging and loose-seal cell-attached electrical recordings from neurons expressing a variety of genetically encoded calcium indicators. CRCNS.org; 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>."},{"issue":"6","key":"ref25","doi-asserted-by":"crossref","first-page":"1328","DOI":"10.1016\/j.neuron.2014.01.019","article-title":"Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior","volume":"81","author":"R Portugues","year":"2014","journal-title":"Neuron"},{"issue":"6","key":"ref26","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1038\/nn.3712","article-title":"Volitional modulation of optically recorded calcium signals during neuroprosthetic learning","volume":"17","author":"KB Clancy","year":"2014","journal-title":"Nat Neurosci"},{"issue":"2","key":"ref27","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1038\/nmeth.3217","article-title":"Simultaneous all-optical manipulation and recording of neural circuit activity with cellular resolution in vivo","volume":"12","author":"AM Packer","year":"2015","journal-title":"Nat Methods"},{"issue":"1","key":"ref28","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.neuron.2015.03.034","article-title":"Closed-loop and activity-guided optogenetic control","volume":"86","author":"L Grosenick","year":"2015","journal-title":"Neuron"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"137","DOI":"10.3389\/fncom.2013.00137","article-title":"Physical principles for scalable neural recording","volume":"7","author":"A Marblestone","year":"2013","journal-title":"Front Comput Neurosci"},{"issue":"1","key":"ref30","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.neuron.2015.03.055","article-title":"Cellular level brain imaging in behaving mammals: an engineering approach","volume":"86","author":"EJO Hamel","year":"2015","journal-title":"Neuron"},{"issue":"3","key":"ref31","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/j.neuron.2016.06.034","article-title":"Wireless recording in the peripheral nervous system with ultrasonic neural dust","volume":"91","author":"D Seo","year":"2016","journal-title":"Neuron"},{"issue":"8","key":"ref32","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1364\/OPTICA.2.000702","article-title":"Decoupled illumination detection in light sheet microscopy for fast volumetric imaging","volume":"2","author":"OE Olarte","year":"2015","journal-title":"Optica"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1214\/09-AOAS303","article-title":"A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data","author":"Y Mishchencko","year":"2011","journal-title":"Ann Appl 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Neurophysiol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.cbpa.2015.05.006","article-title":"The evolving capabilities of rhodopsin-based genetically encoded voltage indicators","volume":"27","author":"Y Gong","year":"2015","journal-title":"Curr Opin Chem Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.cbpa.2015.05.003","article-title":"Designs and sensing mechanisms of genetically encoded fluorescent voltage indicators","volume":"27","author":"F St-Pierre","year":"2015","journal-title":"Curr Opin Chem Biol"},{"issue":"1","key":"ref39","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.cell.2016.05.031","article-title":"Subcellular Imaging of Voltage and Calcium Signals Reveals Neural Processing In Vivo","volume":"166","author":"HH Yang","year":"2016","journal-title":"Cell"},{"key":"ref40","first-page":"1250","article-title":"Adv Neural Inf Process Syst","volume":"26","author":"EA Pnevmatikakis","year":"2013"},{"issue":"2","key":"ref41","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.neuron.2015.12.012","article-title":"Simultaneous multi-plane imaging of neural circuits","volume":"89","author":"W Yang","year":"2016","journal-title":"Neuron"},{"issue":"4","key":"ref42","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1038\/nn.4516","article-title":"Video-rate volumetric functional imaging of the brain at synaptic resolution","volume":"20","author":"R Lu","year":"2017","journal-title":"Nat Neurosci"},{"issue":"4","key":"ref43","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1038\/nmeth.4226","article-title":"Volumetric two-photon imaging of neurons using stereoscopy (vTwINS)","volume":"14","author":"A Song","year":"2017","journal-title":"Nat Methods"},{"issue":"14","key":"ref44","doi-asserted-by":"crossref","first-page":"2007","DOI":"10.1364\/OL.32.002007","article-title":"Aberration-free optical refocusing in high numerical aperture microscopy","volume":"32","author":"EJ Botcherby","year":"2007","journal-title":"Opt Lett"},{"issue":"18","key":"ref45","doi-asserted-by":"crossref","first-page":"21010","DOI":"10.1364\/OE.21.021010","article-title":"Rapid 3D light-sheet microscopy with a tunable lens","volume":"21","author":"FO Fahrbach","year":"2013","journal-title":"Opt Express"},{"issue":"21","key":"ref46","doi-asserted-by":"crossref","first-page":"25418","DOI":"10.1364\/OE.21.025418","article-title":"Wave optics theory and 3-D deconvolution for the light field microscope","volume":"21","author":"M Broxton","year":"2013","journal-title":"Opt Express"},{"issue":"7","key":"ref47","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/nmeth.2964","article-title":"Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy","volume":"11","author":"R Prevedel","year":"2014","journal-title":"Nat Methods"},{"issue":"5","key":"ref48","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1364\/OPTICA.3.000517","article-title":"Compressive light-field microscopy for 3D neural activity recording","volume":"3","author":"NC Pegard","year":"2016","journal-title":"Optica"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"29","DOI":"10.3389\/fnins.2010.00029","article-title":"Two-photon microscopy with diffractive optical elements and spatial light modulators","volume":"4","author":"BO Watson","year":"2010","journal-title":"Front Neurosci"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"5","DOI":"10.3389\/neuro.04.005.2008","article-title":"SLM microscopy: Scanless two-photon imaging and photostimulation using spatial light modulators","volume":"2","author":"V Nikolenko","year":"2008","journal-title":"Front Neural Circuits"},{"issue":"7399","key":"ref51","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1038\/nature11057","article-title":"Brain-wide neuronal dynamics during motor adaptation in zebrafish","volume":"485","author":"MB Ahrens","year":"2012","journal-title":"Nature"},{"key":"ref52","doi-asserted-by":"crossref","unstructured":"Hsieh C, Dhillon I. Fast coordinate descent methods with variable selection for non-negative matrix factorization. In: ACM SIGKDD Int Conf Knowl Discov Data Min 17; 2011. p. 1064\u20131072.","DOI":"10.1145\/2020408.2020577"},{"issue":"6","key":"ref53","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":"J Neurophysiol"},{"issue":"2","key":"ref54","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1137\/090771806","article-title":"Finding structure with randomness: probabilistic algorithms for constructing approximate matrix decompositions","volume":"53","author":"N Halko","year":"2011","journal-title":"SIAM Review"},{"key":"ref55","unstructured":"Giovannucci A, Friedrich J, Deverett B, Staneva V, Chklovskii D, Pnevmatikakis E. CaImAn: An open source toolbox for large scale calcium imaging data analysis on standalone machines; 2017. Cosyne Abstracts 2017, Salt Lake City USA. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/simonsfoundation\/CaImAn\" xlink:type=\"simple\">https:\/\/github.com\/simonsfoundation\/CaImAn<\/ext-link>."},{"key":"ref56","unstructured":"Friedrich J, Soudry D, Mu Y, Freeman J, Ahrens MB, Paninski L. Fast constrained non-negative matrix factorization for whole-brain calcium imaging data. In: NIPS workshop on statistical methods for understanding neural systems; 2015."}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005685","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,8,15]],"date-time":"2017-08-15T00:00:00Z","timestamp":1502755200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005685","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,1]],"date-time":"2019-10-01T20:39:35Z","timestamp":1569962375000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005685"}},"subtitle":[],"editor":[{"given":"Lyle J.","family":"Graham","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,8,3]]},"references-count":56,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2017,8,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005685","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/091132","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,8,3]]}}}