Title |
Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data
|
---|---|
Published in |
Neuron, January 2016
|
DOI | 10.1016/j.neuron.2015.11.037 |
Pubmed ID | |
Authors |
Eftychios A. Pnevmatikakis, Daniel Soudry, Yuanjun Gao, Timothy A. Machado, Josh Merel, David Pfau, Thomas Reardon, Yu Mu, Clay Lacefield, Weijian Yang, Misha Ahrens, Randy Bruno, Thomas M. Jessell, Darcy S. Peterka, Rafael Yuste, Liam Paninski |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 10 | 37% |
Canada | 1 | 4% |
Switzerland | 1 | 4% |
Germany | 1 | 4% |
Japan | 1 | 4% |
Unknown | 13 | 48% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 19 | 70% |
Scientists | 6 | 22% |
Science communicators (journalists, bloggers, editors) | 2 | 7% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 20 | 1% |
France | 4 | <1% |
Japan | 4 | <1% |
Germany | 3 | <1% |
Spain | 3 | <1% |
United Kingdom | 3 | <1% |
China | 3 | <1% |
Netherlands | 2 | <1% |
Switzerland | 2 | <1% |
Other | 7 | <1% |
Unknown | 1492 | 97% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 474 | 31% |
Researcher | 315 | 20% |
Student > Master | 136 | 9% |
Student > Bachelor | 113 | 7% |
Student > Doctoral Student | 91 | 6% |
Other | 196 | 13% |
Unknown | 218 | 14% |
Readers by discipline | Count | As % |
---|---|---|
Neuroscience | 580 | 38% |
Agricultural and Biological Sciences | 313 | 20% |
Engineering | 132 | 9% |
Physics and Astronomy | 69 | 4% |
Computer Science | 47 | 3% |
Other | 147 | 10% |
Unknown | 255 | 17% |