Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data
By Eftychios A. Pnevmatikakis, Daniel Soudry, Yuanjun Gao, Timothy A. Machado, Josh Merel, David Pfau, T. Reardon, Yu Mu, Clay Lacefield, Weijian Yang and 6 more. Neuron, 2016
1,017 citations recorded by the source corpus.
SUMMARY 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 multineuronal imaging data, whole-brain light-sheet imaging data, and dendritic imaging data.
Subfields: Biophysics, Radiology, Nuclear Medicine and Imaging
View Paper: https://www.semanticscholar.org/paper/879d35a88b92dd1da1c7363738c1ce042efb0ba5
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In Biophysics
Citations in the corpus
- A dedicated population for reward coding in the hippocampus (2018, methodology): “Within each block, the shapes of active cells were identified using constrained nonnegative matrix factorization (Pnevmatikakis et al., 2016).”
- Shared cortex-cerebellum dynamics in the execution and learning of a motor task (2019, neutral): “…and Algorithms MATLAB Mathworks https://www.mathworks.com IMARIS Bitplane https://www.bitplane.com CNMF Simons Foundation/Flatiron institute; Pnevmatikakis et al., 2016 https://github.com/flatironinstitute/CaImAn-MATLAB NoRMCorre Simons Foundation/Flatiron institute; Pnevmatikakis and…”
- Dynamic Reorganization of Neuronal Activity Patterns in Parietal Cortex. (2017, neutral): “…Vidrio Technologies http://scanimage.vidriotechnologies.com Calcium imaging deconvolution algorithm (Pnevmatikakis et al., 2016) https://github.com/epnev/constrained-foopsi ViRMEn (Virtual Reality Mouse Engine) (Aronov and Tank, 2014)…”
- NoRMCorre: An online algorithm for piecewise rigid motion correction of calcium imaging data (2017, methodology): “243 This package complements and will be integrated with the CNMF Matlab 244 package for demixing and deconvolution of registered movies [13] available at 245 https://github.”
- Fast and sensitive GCaMP calcium indicators for imaging neural populations (2021, neutral): “05) and comparable to 8m (84[32-165] ms) and XCaMP-Gf (91[48-155] ms) (Fig.”
- Electrical and synaptic integration of glioma into neural circuits (2019, neutral): “The correlation image for each pixel is computed by averaging the correlation coefficients (taken over time) of each pixel with its four immediate neighbors 50 .”
- Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data (2018, neutral): “Here, si is the standard deviation of the noise at xi and its value can be estimated using the power spectral density (PSD) method (Pnevmatikakis et al., 2016).”
- Simultaneous multi-plane imaging of neural circuits (2016, neutral): “The raw images are motion corrected using a pyramid approach (Thevenaz et al., 1998), and analyzed using a novel constrained non-negative matrix factorization algorithm detailed in the companion paper (Pnevmatikakis et al., 2016), coded in MATLAB.”