Related papers: A structured matrix factorization framework for la…
Calcium imaging has revolutionized systems neuroscience, providing the ability to image large neural populations with single-cell resolution. The resulting datasets are quite large, which has presented a barrier to routine open sharing of…
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…
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…
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…
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…
Recently, fluorescence-based optical techniques have emerged as a powerful tool to probe information in the mammalian brain. However, tissue heterogeneities prevent clear imaging of deep neuron bodies due to light scattering. While several…
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…
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 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,…
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…
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…
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,…
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…
The success and generalisation of deep learning algorithms heavily depend on learning good feature representations. In medical imaging this entails representing anatomical information, as well as properties related to the specific imaging…
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,…
Recently, convex formulations of low-rank matrix factorization problems have received considerable attention in machine learning. However, such formulations often require solving for a matrix of the size of the data matrix, making it…
An optical flow gradient algorithm was applied to spontaneously forming net- works of neurons and glia in culture imaged by fluorescence optical microscopy in order to map functional calcium signaling with single pixel resolution. Optical…
Multiresolution analysis and matrix factorization are foundational tools in computer vision. In this work, we study the interface between these two distinct topics and obtain techniques to uncover hierarchical block structure in symmetric…
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…
The proposed article aims at offering a comprehensive tutorial for the computational aspects of structured matrix and tensor factorization. Unlike existing tutorials that mainly focus on {\it algorithmic procedures} for a small set of…