title: Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data.
abstract: We present a modular approach for analyzing calcium imaging recordings of large neuronal ensembles. Our goal is to simultaneously identify the locations of the neurons, demix spatially overlapping components, and denoise and deconvolve the spiking activity from the slow dynamics of the calcium indicator. Our approach relies on a constrained nonnegative matrix factorization that expresses the spatiotemporal fluorescence activity as the product of a spatial matrix that encodes the spatial footprint of each neuron in the optical field and a temporal matrix that characterizes the calcium concentration of each neuron over time. This framework is combined with a novel constrained deconvolution approach that extracts estimates of neural activity from fluorescence traces, to create a spatiotemporal processing algorithm that requires minimal parameter tuning. We demonstrate the general applicability of our method by applying it to in vitro and in vivo multi-neuronal imaging data, whole-brain light-sheet imaging data, and dendritic imaging data.
authors.affiliation: Center for Computational Biology, Simons Foundation, New York, NY 10010, USA; Department of Statistics, Center for Theoretical Neuroscience, and Grossman Center for the Statistics of Mind, Columbia University, New York, NY 10027, USA. Electronic address: epnevmatikakis@simonsfoundation.org.
authors.forename: Eftychios A
authors.initials: EA
authors.lastname: Pnevmatikakis
authors.affiliation: Department of Statistics, Center for Theoretical Neuroscience, and Grossman Center for the Statistics of Mind, Columbia University, New York, NY 10027, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Soudry
authors.affiliation: Department of Statistics, Center for Theoretical Neuroscience, and Grossman Center for the Statistics of Mind, Columbia University, New York, NY 10027, USA.
authors.forename: Yuanjun
authors.initials: Y
authors.lastname: Gao
authors.affiliation: Department of Statistics, Center for Theoretical Neuroscience, and Grossman Center for the Statistics of Mind, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics and Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Neuroscience and Kavli Institute of Brain Science, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10032, USA.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Machado
authors.affiliation: Department of Statistics, Center for Theoretical Neuroscience, and Grossman Center for the Statistics of Mind, Columbia University, New York, NY 10027, USA; Department of Neuroscience and Kavli Institute of Brain Science, Columbia University, New York, NY 10032, USA.
authors.forename: Josh
authors.initials: J
authors.lastname: Merel
authors.affiliation: Department of Statistics, Center for Theoretical Neuroscience, and Grossman Center for the Statistics of Mind, Columbia University, New York, NY 10027, USA; Department of Neuroscience and Kavli Institute of Brain Science, Columbia University, New York, NY 10032, USA.
authors.forename: David
authors.initials: D
authors.lastname: Pfau
authors.affiliation: Department of Biochemistry and Molecular Biophysics and Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Neuroscience and Kavli Institute of Brain Science, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10032, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Reardon
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Mu
authors.affiliation: Department of Neuroscience and Kavli Institute of Brain Science, Columbia University, New York, NY 10032, USA.
authors.forename: Clay
authors.initials: C
authors.lastname: Lacefield
authors.affiliation: Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
authors.forename: Weijian
authors.initials: W
authors.lastname: Yang
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA.
authors.forename: Misha
authors.initials: M
authors.lastname: Ahrens
authors.affiliation: Department of Neuroscience and Kavli Institute of Brain Science, Columbia University, New York, NY 10032, USA.
authors.forename: Randy
authors.initials: R
authors.lastname: Bruno
authors.affiliation: Department of Biochemistry and Molecular Biophysics and Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Neuroscience and Kavli Institute of Brain Science, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10032, USA.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Jessell
authors.affiliation: Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10032, USA; Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
authors.forename: Darcy S
authors.initials: DS
authors.lastname: Peterka
authors.affiliation: Department of Neuroscience and Kavli Institute of Brain Science, Columbia University, New York, NY 10032, USA; Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
authors.forename: Rafael
authors.initials: R
authors.lastname: Yuste
authors.affiliation: Department of Statistics, Center for Theoretical Neuroscience, and Grossman Center for the Statistics of Mind, Columbia University, New York, NY 10027, USA; Department of Neuroscience and Kavli Institute of Brain Science, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10032, USA; Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Electronic address: liam@stat.columbia.edu.
authors.forename: Liam
authors.initials: L
authors.lastname: Paninski
mesh_terms: D000200:Action Potentials / Q000502:physiology*; D000818:Animals; D002118:Calcium / Q000032:analysis / Q000378:metabolism*; D003712:Dendrites / Q000737:chemistry / Q000378:metabolism; D005456:Fluorescent Dyes / Q000032:analysis / Q000378:metabolism; D051379:Mice; D008810:Mice, Inbred C57BL; D008856:Microscopy, Fluorescence / Q000379:methods*; D009474:Neurons / Q000737:chemistry / Q000378:metabolism*; D013223:Statistics as Topic / Q000379:methods*
chemical_list: D005456:Fluorescent Dyes; D002118:Calcium