Related papers: realSEUDO for real-time calcium imaging analysis
Miniaturized calcium imaging is an emerging neural recording technique that has been widely used for monitoring neural activity on a large scale at a specific brain region of rats or mice. Most existing calcium-image analysis pipelines…
Calcium imaging is one of the most important tools in neurophysiology as it enables the observation of neuronal activity for hundreds of cells in parallel and at single-cell resolution. In order to use the data gained with calcium imaging,…
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…
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…
Deducing the structure of neural circuits is one of the central problems of modern neuroscience. Recently-introduced calcium fluorescent imaging methods permit experimentalists to observe network activity in large populations of neurons,…
We present PSEUDo, an adaptive feature learning technique for exploring visual patterns in multi-track sequential data. Our approach is designed with the primary focus to overcome the uneconomic retraining requirements and inflexible…
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…
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…
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…
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 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…
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…
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 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…
Virtual studies of ICD behaviour are crucial for testing device functionality in a controlled environment prior to clinical application. Although previous works have shown the viability of using in silico testing for diagnosis, there is a…
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…
Fluorescence Microcopy Calcium Imaging is a fundamental tool to in-vivo record and analyze large scale neuronal activities simultaneously at a single cell resolution. Automatic and precise detection of behaviorally relevant neuron activity…
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…
Motion correction is the first in a pipeline of algorithms to analyze calcium imaging videos and extract biologically relevant information, for example the network structure of the neurons therein. Fast motion correction would be especially…
Methods: We have developed a software suite (DataSet Tracker) for real-time analysis designed to run on computers, smartphones, and smart glasses hardware and suitable for resource-constrained, on-the-fly computing in microscopes without…