Fast online deconvolution of calcium imaging data

By Johannes Friedrich, Pengcheng Zhou, Liam Paninski. PLoS Comput. Biol., 2016

542 citations recorded by the source corpus.

Fluorescent calcium indicators are a popular means for observing the spiking activity of large neuronal populations, but extracting the activity of each neuron from raw fluorescence calcium imaging data is a nontrivial problem. We present a fast online active set method to solve this sparse non-negative deconvolution problem. Importantly, the algorithm 3progresses through each time series sequentially from beginning to end, thus enabling real-time online estimation of neural activity during the imaging session. Our algorithm is a generalization of the pool adjacent violators algorithm (PAVA) for isotonic regression and inherits its linear-time computational complexity. We gain remarkable increases in processing speed: more than one order of magnitude compared to currently employed state of the art convex solvers relying on interior point methods. Unlike these approaches, our method can exploit warm starts; therefore optimizing model hyperparameters only requires a handful of passes through the data. A minor modification can further improve the quality of activity inference by imposing a constraint on the minimum spike size. The algorithm enables real-time simultaneous deconvolution of O(105) traces of whole-brain larval zebrafish imaging data on a laptop.

Subfields: Biophysics, Electrical and Electronic Engineering

View Paper: https://www.semanticscholar.org/paper/f6c2e790ca208960087a35fc2e3853af7aad7282

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Citations in the corpus

Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data (2018, unknown): “The spatial patches can be deter- mined using a mildly dilated version of the support of the previous estimate of A (Pnevmatikakis et al., 2016; Friedrich et al., 2017a).”
CaImAn an open source tool for scalable calcium imaging data analysis (2019, methodology): “, 2016) and implemented using the near-online OASIS algorithm (Friedrich et al., 2017b).”
Spontaneous Behaviors Drive Multidimensional, Brain-wide Activity (2019, methodology): “After neuropil subtraction, we subtracted a running baseline of the calcium traces with a sliding window of 60 s to remove long time scale drift in baseline, then applied nonnegative spike deconvolution using the OASIS algorithm with a fixed time scale of calcium indicator decay of 2 s (58, 59).”
Suite2p: beyond 10,000 neurons with standard two-photon microscopy (2016, methodology): “However, based on a quantitative comparison of multiple methods 24 , we recommend by default unconstrained non-negative deconvolution using exponential kernels 25–27 with a kernel decay timescale that matches the value reported in the literature for the particular calcium sensor used.”