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A fundamental challenge in calcium imaging has been to infer the timing of action potentials from the measured noisy calcium fluorescence traces. We systematically evaluate a range of spike inference algorithms on a large benchmark dataset…
Two-photon imaging of calcium indicators allows simultaneous recording of responses of hundreds of neurons over hours and even days, but provides a relatively indirect measure of their spiking activity. Existing deconvolution algorithms…
In recent years, a number of methods have been proposed to estimate the times at which a neuron spikes on the basis of calcium imaging data. However, quantifying the uncertainty associated with these estimated spikes remains an open…
In recent years, new technologies in neuroscience have made it possible to measure the activities of large numbers of neurons simultaneously in behaving animals. For each neuron, a fluorescence trace is measured; this can be seen as a…
Recent advancements in miniaturized fluorescence microscopy have made it possible to investigate neuronal responses to external stimuli in awake behaving animals through the analysis of intra-cellular calcium signals. An on-going challenge…
Calcium imaging permits optical measurement of neural activity. Since intracellular calcium concentration is an indirect measurement of neural activity, computational tools are necessary to infer the true underlying spiking activity from…
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…
Neurons encode information about the environment through their activity. As animals explore the environment, neurons rapidly acquire selectivity for distinct features of the external world; characterizing how these selectivity patterns…
Understanding how neurons coordinate their activity is a fundamental question in neuroscience, with implications for learning, memory, and neurological disorders. Calcium imaging has emerged as a powerful method to observe large-scale…
We present efficient Bayesian methods for extracting neuronal spiking information from calcium imaging data. The goal of our methods is to sample from the posterior distribution of spike trains and model parameters (baseline concentration,…
We study noisy calcium imaging data, with a focus on the classification of spike traces. As raw traces obscure the true temporal structure of neuron's activity, we performed a tuned filtering of the calcium concentration using two methods:…
Calcium imaging for observing spiking activity from large populations of neurons are quickly gaining popularity. While the raw data are fluorescence movies, the underlying spike trains are of interest. This work presents a fast non-negative…
We present a structured matrix factorization approach to analyzing calcium imaging recordings of large neuronal ensembles. Our goal is to simultaneously identify the locations of the neurons, demix spatially overlapping components, and…
Quantification of neuronal correlations in neuron populations helps us to understand neural coding rules. Such quantification could also reveal how neurons encode information in normal and disease conditions like Alzheimer's and…
Calcium imaging has become a fundamental neural imaging technique, aiming to recover the individual activity of hundreds of neurons in a cortical region. Current methods (mostly matrix factorization) are aimed at detecting neurons in the…
Calcium imaging allows for the parallel measurement of large neuronal populations in a spatially resolved and minimally invasive manner, and has become a gold-standard for neuronal functionality. While deep generative models have been…
With the increasing popularity of calcium imaging data in neuroscience research, methods for analyzing calcium trace data are critical to address various questions. The observed calcium traces are either analyzed directly or deconvolved to…
We address the problem of finding patterns from multi-neuronal spike trains that give us insights into the multi-neuronal codes used in the brain and help us design better brain computer interfaces. We focus on the synchronous firings of…
Advances in neuroscience have enabled researchers to measure the activities of large numbers of neurons simultaneously in behaving animals. We have access to the fluorescence of each of the neurons which provides a first-order approximation…
Fluorescent calcium imaging provides a potentially powerful tool for inferring connectivity in neural circuits with up to thousands of neurons. However, a key challenge in using calcium imaging for connectivity detection is that current…