Related papers: Quantifying uncertainty in spikes estimated from c…
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,…
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…
Optical imaging of genetically encoded calcium indicators is a powerful tool to record the activity of a large number of neurons simultaneously over a long period of time from freely behaving animals. However, determining the exact time at…
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…
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…
Quantification of information content and its temporal variation in intracellular calcium spike trains in neurons helps one understand functions such as memory, learning, and cognition. Such quantification could also reveal pathological…
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…
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…
In this work, we propose a simple yet effective solution to the problem of connectome inference in calcium imaging data. The proposed algorithm consists of two steps. First, processing the raw signals to detect neural peak activities.…
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…
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…
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 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 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…
In the past few years, new technologies in the field of neuroscience have made it possible to simultaneously image activity in large populations of neurons at cellular resolution in behaving animals. In mid-2016, a huge repository of this…
Calcium imaging is an important technique for monitoring the activity of thousands of neurons simultaneously. As calcium imaging datasets grow in size, automated detection of individual neurons is becoming important. Here we apply a…
Plasticity is one of the most important properties of the nervous system, which enables animals to adjust their behavior to the ever-changing external environment. Changes in synaptic efficacy between neurons constitute one of the major…
The presynaptic free calcium dynamics of neurons due to various stimulation protocols is investigated in a mathematical model. The model includes calcium influx through voltage-dependent calcium channels, calcium buffering by endogenous and…
Identification of patterns from discrete data time-series for statistical inference, threat detection, social opinion dynamics, brain activity prediction has received recent momentum. In addition to the huge data size, the associated…
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…