Title: Fast Nonconvex Deconvolution of Calcium Imaging Data,
Abstract: Calcium imaging data promises to transform the field of neuroscience by
making it possible to record from large populations of neurons simultaneously.
However, determining the exact moment in time at which a neuron spikes, from a
calcium imaging data set, amounts to a non-trivial deconvolution problem which
is of critical importance for downstream analyses. While a number of
formulations have been proposed for this task in the recent literature, in this
paper we focus on a formulation recently proposed in Jewell and Witten (2017)
which has shown initial promising results. However, this proposal is slow to
run on fluorescence traces of hundreds of thousands of timesteps.
Here we develop a much faster online algorithm for solving the optimization
problem of Jewell and Witten (2017) that can be used to deconvolve a
fluorescence trace of 100,000 timesteps in less than a second. Furthermore,
this algorithm overcomes a technical challenge of Jewell and Witten (2017) by
avoiding the occurrence of so-called "negative" spikes. We demonstrate that
this algorithm has superior performance relative to existing methods for spike
deconvolution on calcium imaging datasets that were recently released as part
of the spikefinder challenge (this http URL).
Our C++ implementation, along with R and python wrappers, is publicly
available on Github at this https URL.