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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…
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 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 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…
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 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…
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…
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 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…
Cells use biochemical networks to translate environmental information into intracellular responses. These responses can be highly dynamic, but how the information is encoded in these dynamics remains poorly understood. Here we investigate…
Unicellular organisms are open metabolic systems that need to process information about their external environment in order to survive. In most types of tissues and organisms, cells use calcium signaling to carry information from the…
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,…
Calcium imaging is a technique for observing neuron activity as a series of images showing indicator fluorescence over time. Manually segmenting neurons is time-consuming, leading to research on automated calcium imaging segmentation…
Neural systems can be modeled as networks of functionally connected neural elements. The resulting network can be analyzed using mathematical tools from network science and graph theory to quantify the system's topological organization and…
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…
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…
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…
The ability to acquire large-scale recordings of neuronal activity in awake and unrestrained animals poses a major challenge for studying neural coding of animal behavior. We present a new instrument capable of recording intracellular…
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…