Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data

Details

• Alternative Title:
  Neuron
• Personal Author:
  Pnevmatikakis, Eftychios A. ; Soudry, Daniel ; Gao, Yuanjun ; Machado, Timothy A. ; Merel, Josh ; Pfau, David ; Reardon, Thomas ; Mu, Yu ; Lacefield, Clay ; Yang, Weijian ; Ahrens, Misha ; Bruno, Randy ; Jessell, Thomas M. ; Peterka, Darcy S. ; Yuste, Rafael ; Paninski, Liam
• Description:
  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.
• Subjects:
  Action Potentials Animals Calcium Dendrites Fluorescent Dyes Mice Mice, Inbred C57BL Microscopy, Fluorescence Neurons Statistics As Topic
• Source:
  Neuron. 89(2):285-299.
• Pubmed ID:
  26774160
• Pubmed Central ID:
  PMC4881387
• Document Type:
  Journal Article
• Funding:
  5R21DA034195/DA/NIDA NIH HHS/United States ; R01 MH101218/MH/NIMH NIH HHS/United States ; DP1 EY024503/EY/NEI NIH HHS/United States ; R21NS081393/NS/NINDS NIH HHS/United States ; 1R01MH101218/MH/NIMH NIH HHS/United States ; R01 EY011787/EY/NEI NIH HHS/United States ; R41MH100895/MH/NIMH NIH HHS/United States ; R41 MH100895/MH/NIMH NIH HHS/United States ; R21 NS081393/NS/NINDS NIH HHS/United States ; DP1EY024503/DP/NCCDPHP CDC HHS/United States ; R01EY011787/EY/NEI NIH HHS/United States ; R21 DA034195/DA/NIDA NIH HHS/United States
• Volume:
  89
• Issue:
  2
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:c44eeb5d3759df2269cce77345ec8cf4522b5f6b945b7bce2f6df1326b2c5fb5
• Download URL:
  https://stacks.cdc.gov/view/cdc/39625/cdc_39625_DS1.pdf
• File Type:
  [PDF - 1.21 MB ]