Related papers: Simple connectome inference from partial correlati…
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…
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…
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:…
Functional connectomes capture brain interactions via synchronized fluctuations in the functional magnetic resonance imaging signal. If measured during rest, they map the intrinsic functional architecture of the brain. With task-driven…
This article presents a review of computational methods for connectivity inference from neural activity data derived from multi-electrode recordings or fluorescence imaging. We first identify biophysical and technical challenges in…
Brain connectomics is a developing field in neurosciences which strives to understand cognitive processes and psychiatric diseases through the analysis of interactions between brain regions. However, in the high-dimensional, low-sample, and…
Calcium imaging has emerged as a workhorse method in neuroscience to investigate patterns of neuronal activity. Instrumentation to acquire calcium imaging movies has rapidly progressed and has become standard across labs. Still, algorithms…
The recent development of genetically encoded calcium indicators enables monitoring in vivo the activity of neuronal populations. Most analysis of these calcium transients relies on linear regression analysis based on the sensory stimulus…
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…
Connected networks are a fundamental structure of neurobiology. Understanding these networks will help us elucidate the neural mechanisms of computation. Mathematically speaking these networks are `graphs' - structures containing objects…
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…
Coronary artery calcium (CAC) is a significant marker of atherosclerosis and cardiovascular events. In this work we present a system for the automatic quantification of calcium score in ECG-triggered non-contrast enhanced cardiac computed…
Functional connectivity (FC) refers to the investigation of interactions between brain regions to understand integration of neural activity in several regions. FC is often estimated using functional magnetic resonance images (fMRI). There…
With modern calcium imaging technology, activities of thousands of neurons can be recorded in vivo. These experiments can potentially provide new insights into intrinsic functional neuronal connectivity, defined as contemporaneous…
High-throughput methods for yielding the set of connections in a neural system, the connectome, are now being developed. This tutorial describes ways to analyze the topological and spatial organization of the connectome at the macroscopic…
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…
In vivo calcium imaging through microscopes has enabled deep brain imaging of previously inaccessible neuronal populations within the brains of freely moving subjects. However, microendoscopic data suffer from high levels of background…
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…
Estimating causal interactions in the brain from functional magnetic resonance imaging (fMRI) data remains a challenging task. Multiple studies have demonstrated that all current approaches to determine direction of connectivity perform…
The connectome, a map of the structural and/or functional connections in the brain, provides a complex representation of the neurobiological phenotypes on which it supervenes. This information-rich data modality has the potential to…