{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T01:54:13Z","timestamp":1774058053219,"version":"3.50.1"},"reference-count":55,"publisher":"Public Library of Science (PLoS)","issue":"5","content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000379","type":"journal-article","created":{"date-parts":[[2009,5,7]],"date-time":"2009-05-07T21:02:23Z","timestamp":1241730143000},"page":"e1000379","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":73,"title":["Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings"],"prefix":"10.1371","volume":"5","author":[{"given":"Quentin J. M.","family":"Huys","sequence":"first","affiliation":[]},{"given":"Liam","family":"Paninski","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2009,5,8]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1016\/S0006-3495(91)82099-9","article-title":"Voltage-sensitive dye recording of action potentials and synaptic potentials from sympathetic microcultures.","volume":"60","author":"CB Chien","year":"1991","journal-title":"Biophys J"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"6703","DOI":"10.1523\/JNEUROSCI.0307-04.2004","article-title":"Voltage imaging from dendrites of mitral cells: EPSP attenuation and spike trigger zones.","volume":"24","author":"M Djurisic","year":"2004","journal-title":"J Neurosci"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1007\/s10571-005-3059-6","article-title":"Imaging brain activity with voltage- and calcium-sensitive dyes.","volume":"25","author":"BJ Baker","year":"2005","journal-title":"Cell Mol Neurobiol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1073\/pnas.0510092103","article-title":"Imaging membrane potential in dendritic spines.","volume":"103","author":"M Nuriya","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1113\/jphysiol.2006.125005","article-title":"Dendritic signals from rat hippocampal CA1 pyramidal neurons during coincident pre- and post-synaptic activity: a combined voltage- and calciumimaging study.","volume":"580","author":"M Canepari","year":"2007","journal-title":"J Physiol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1007\/s00424-006-0149-3","article-title":"Imaging membrane potential in dendrites and axons of single neurons.","volume":"453","author":"GJ Stuart","year":"2006","journal-title":"Pflugers Arch"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1023\/A:1008935410038","article-title":"On sequential Monte Carlo sampling methods for Bayesian filtering.","volume":"10","author":"A Doucet","year":"2000","journal-title":"Stat Comput"},{"key":"ref8","first-page":"64","article-title":"Comparison of Resampling Schemes for Particle Filtering.","author":"R Douc","year":"2005"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1152\/jn.1991.66.2.635","article-title":"A model of a CA3 hippocampal pyramidal neuron incorporating voltage-clamp data on intrinsic conductances.","volume":"66","author":"RD Traub","year":"1991","journal-title":"J Neurophysiol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1016\/S0896-6273(03)00148-X","article-title":"Arithmetic of subthreshold synaptic summation in a model CA1 pyramidal cell.","volume":"37","author":"P Poirazi","year":"2003","journal-title":"Neuron"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"3143","DOI":"10.1152\/jn.00046.2003","article-title":"Coincidence detection in pyramidal neurons is tuned by their dendritic branching pattern.","volume":"89","author":"AT Schaefer","year":"2003","journal-title":"J Neurophysiol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1948","DOI":"10.1152\/jn.1993.69.6.1948","article-title":"Exploring parameter space in detailed single neuron models: Simulations of the mitral and granule cells of the olfactory bulb.","volume":"69","author":"US Bhalla","year":"1993","journal-title":"J Neurophysiol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1023\/A:1008887028637","article-title":"On the use of Bayesian methods for evaluating compartmental neural models.","volume":"5","author":"P Baldi","year":"1998","journal-title":"J Comput Neurosci"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1023\/A:1008972005316","article-title":"A comparative survey of automated parameter-search methods for compartmental neural models.","volume":"7","author":"MC Vanier","year":"1999","journal-title":"J Comput Neurosci"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"3998","DOI":"10.1152\/jn.00641.2003","article-title":"Hand-tuning conductance-based models: Construction and analysis of databases of model neurons.","volume":"90","author":"AA Prinz","year":"2003","journal-title":"J Neurophysiol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1152\/jn.00190.2004","article-title":"Generalized integrate-and-fire models of neuronal activity approximate spike trains of a detailed model to a high degree of accuracy.","volume":"92","author":"R Jolivet","year":"2004","journal-title":"J Neurophysiol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"3730","DOI":"10.1152\/jn.00408.2005","article-title":"Constraining compartmental models using multiple voltage recordings and genetic algorithms.","volume":"94","author":"N Keren","year":"2005","journal-title":"J Neurophysiol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1016\/j.neunet.2005.06.038","article-title":"Optimizing conductance parameters of cortical neural models via electrotonic partitions.","volume":"18","author":"K Bush","year":"2005","journal-title":"Neural Netw"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"e94","DOI":"10.1371\/journal.pcbi.0020094","article-title":"Complex parameter landscape for a complex neuron model.","volume":"2","author":"P Achard","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"ref20","first-page":"1","article-title":"Neurofitter: a parameter tuning package for a wide range of electrophysiological neuron models.","volume":"1","author":"WV Geit","year":"2007","journal-title":"Front Neuroinformatics"},{"key":"ref21","article-title":"Parameter space reduction in neuron model optimization through minimization of residual voltage clamp current.","author":"TM Morse","year":"2001"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1016\/j.neucom.2004.01.174","article-title":"A novel parameter optimisation technique for compartmental models applied to a model of a striatal medium spiny neuron.","volume":"58\u201360","author":"R Wood","year":"2004","journal-title":"Neurocomputing"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1152\/jn.00079.2006","article-title":"Efficient estimation of detailed single-neuron models.","volume":"96","author":"QJM Huys","year":"2006","journal-title":"J Neurophysiol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.2517-6161.1977.tb01600.x","article-title":"Maximum Likelihood from Incomplete Data via the EM Algorithm.","volume":"39","author":"A Dempster","year":"1977","journal-title":"J Royal Stat Soc Series B (Methodological)"},{"key":"ref25","article-title":"Information theory, inference and learning algorithms","author":"DJ MacKay","year":"2003"},{"key":"ref26","article-title":"Biophysics of Computation.","author":"C Koch","year":"1999"},{"key":"ref27","article-title":"Theoretical Neuroscience. Computational Neuroscience","author":"P Dayan","year":"2001"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1113\/jphysiol.1952.sp004764","article-title":"A quantitative description of membrane current and its application to conduction and excitation in nerve.","volume":"117","author":"AL Hodgkin","year":"1952","journal-title":"J Physiol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1111\/j.1469-7793.2001.00445.x","article-title":"Compartmental models of rat cerebellar purkinje cells based on simultaneous somatic and dendritic patch-clamp recordings.","volume":"535","author":"A Roth","year":"2001","journal-title":"J Physiol"},{"key":"ref30","article-title":"Learning nonlinear dynamical systems using an EM algorithm.","author":"S Roweis","year":"1998"},{"key":"ref31","first-page":"672","article-title":"Optimization with EM and Expectation-Conjugate-Gradient.","author":"R Salakhutdinov","year":"2003"},{"key":"ref32","article-title":"Spike inference from calcium imaging using sequential monte carlo methods.","author":"J Vogelstein","year":"2008","journal-title":"Biophys J"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1162\/neco.2007.19.4.1097","article-title":"State-Space Models: From the EM Algorithm to a Gradient Approach.","volume":"19","author":"R Olsson","year":"2007","journal-title":"Neural Computation"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1196\/annals.1342.009","article-title":"Imaging of spiking and subthreshold activity of mitral cells with voltage-sensitive dyes.","volume":"1048","author":"M Djurisic","year":"2005","journal-title":"Ann N Y Acad Sci"},{"key":"ref35","article-title":"Fast functional imaging of single neurons using randomaccess multiphoton (RAMP) microscopy.","author":"V Iyer","year":"2005","journal-title":"J Neurophysiol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1016\/j.conb.2006.08.011","article-title":"New methods and uses for fast optical scanning.","volume":"16","author":"P Saggau","year":"2006","journal-title":"Curr Opin Neurobiol"},{"key":"ref37","article-title":"Time Series Analysis by State Space Methods","author":"J Durbin","year":"2001"},{"key":"ref38","first-page":"318","article-title":"Sharp failure rates for the bootstrap particle filter in high dimensions.","volume":"3","author":"P Bickel","year":"2008","journal-title":"IMS Collections"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1023\/B:JCNS.0000023869.22017.2e","article-title":"Modeldb: A database to support computational neuroscience.","volume":"17","author":"ML Hines","year":"2004","journal-title":"J Comput Neurosci"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"2361","DOI":"10.1152\/jn.90332.2008","article-title":"Role of axonal NaV1.6 sodium channels in action potential initiation of CA1 pyramidal neurons.","volume":"100","author":"M Royeck","year":"2008","journal-title":"J Neurophysiol"},{"key":"ref41","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511815706","article-title":"Spiking Neuron Models: Single Neurons, Populations, Plasticity","author":"W Gerstner","year":"2002"},{"key":"ref42","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4899-4473-3","article-title":"Nonparametric regression and generalized linear models","author":"PJ Green","year":"1994"},{"key":"ref43","article-title":"A new look at state-space models for neural data.","author":"L Paninski","year":"2009","journal-title":"J Comp Neuro Under Review"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1016\/j.neuroimage.2006.08.035","article-title":"Variational free energy and the Laplace approximation.","volume":"34","author":"K Friston","year":"2007","journal-title":"Neuroimage"},{"key":"ref45","article-title":"Identification and comparison of stochastic metabolic\/hemodynamic models (sMHM) for the generation of the BOLD signal.","author":"R Sotero","year":"2008","journal-title":"J Comput Neurosci"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3389\/neuro.01.1.1.001.2007","article-title":"A novel multiple objective optimization framework for constraining conductance-based neuron models by experimental data.","volume":"1","author":"S Druckmann","year":"2007","journal-title":"Front Neurosci"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1007\/s00422-008-0269-2","article-title":"Evaluating automated parameter constraining procedures of neuron models by experimental and surrogate data.","volume":"99","author":"S Druckmann","year":"2008","journal-title":"Biol Cybern"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1002\/0471221546.ch7","article-title":"The Unscented Kalman Filter.","author":"E Wan","year":"2001","journal-title":"Kalman Filtering and Neural Networks"},{"key":"ref49","doi-asserted-by":"crossref","DOI":"10.1117\/12.280797","article-title":"A new extension of the Kalman filter to nonlinear systems.","author":"S Julier","year":"1997"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1016\/S1053-8119(03)00071-5","article-title":"Variational Bayesian inference for fMRI time series.","volume":"19","author":"W Penny","year":"2003","journal-title":"Neuroimage"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1111\/j.1467-9892.2005.00454.x","article-title":"An approximate innovation method for the estimation of diffusion processes from discrete data.","volume":"27","author":"J Jimenez","year":"2006","journal-title":"Journal of Time Series Analysis"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1016\/j.neuroimage.2003.09.052","article-title":"A state-space model of the hemodynamic approach: nonlinear filtering of BOLD signals.","volume":"21","author":"JJ Riera","year":"2004","journal-title":"Neuroimage"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1152\/jn.00412.2001","article-title":"Failure of averaging in the construction of a conductance-based neuron model.","volume":"87","author":"J Golowasch","year":"2002","journal-title":"J Neurophysiol"},{"key":"ref54","article-title":"Monte Carlo Strategies in Scientific Computing.","author":"J Liu","year":"2002"},{"key":"ref55","article-title":"Model-based optimal interpolation and filtering for noisy, intermittent biophysical recordings.","author":"QJM Huys","year":"2006"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000379","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,19]],"date-time":"2019-05-19T22:57:30Z","timestamp":1558306650000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000379"}},"subtitle":[],"editor":[{"given":"Karl J.","family":"Friston","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2009,5,8]]},"references-count":55,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2009,5,8]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000379","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,5,8]]}}}