Spontaneous behaviors drive multidimensional, brainwide activity

Science, Journal Year: 2019, Volume and Issue: 364(6437)

Published: April 19, 2019

Neuron activity across the brain How is it that groups of neurons dispersed through interact to generate complex behaviors? Three papers in this issue present brain-scale studies neuronal and dynamics (see Perspective by Huk Hart). Allen et al. found thirsty mice, there widespread neural related stimuli elicit licking drinking. Individual encoded task-specific responses, but every area contained with different types response. Optogenetic stimulation thirst-sensing one reinstated drinking previously signaled thirst. Gründemann investigated mouse basal amygdala relation behavior during tasks. Two ensembles showed orthogonal exploratory nonexploratory behaviors, possibly reflecting levels anxiety experienced these areas. Stringer analyzed spontaneous firing, finding primary visual cortex both information motor facial movements. The variability responses mainly arousal reflects encoding latent behavioral states. Science , p. eaav3932 eaav8736 eaav7893 ; see also 236

Language: Английский

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Suite2p: beyond 10,000 neurons with standard two-photon microscopy

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2016, Volume and Issue: unknown

Published: June 30, 2016

Abstract Two-photon microscopy of calcium-dependent sensors has enabled unprecedented recordings from vast populations neurons. While the and microscopes have matured over several generations development, computational methods to process resulting movies remain inefficient can give results that are hard interpret. Here we introduce Suite2p: a fast, accurate complete pipeline registers raw movies, detects active cells, extracts their calcium traces infers spike times. Suite2p runs on standard workstations, operates faster than real time, recovers ~2 times more cells previous state-of-the-art method. Its low load allows routine detection ~10,000 simultaneously with two-photon resonant-scanning microscopes. Recordings at this scale promise reveal fine structure activity in large neurons or subcellular structures such as synaptic boutons.

Language: Английский

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CaImAn an open source tool for scalable calcium imaging data analysis

eLife, Journal Year: 2019, Volume and Issue: 8

Published: Jan. 14, 2019

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. We present CaImAn, an open-source library for calcium imaging analysis. CaImAn provides automatic methods address problems common pre-processing, including motion correction, neural activity identification, registration across different sessions collection. It does this while requiring minimal user intervention, good scalability on computers ranging from laptops high-performance computing clusters. is suitable two-photon one-photon imaging, also enables real-time streaming data. To benchmark performance we collected combined a corpus manual annotations multiple labelers nine mouse datasets. demonstrate achieves near-human detecting locations active neurons.

Language: Английский

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Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data

eLife, Journal Year: 2018, Volume and Issue: 7

Published: Feb. 22, 2018

In vivo calcium imaging through microendoscopic lenses enables of previously inaccessible neuronal populations deep within the brains freely moving animals. However, it is computationally challenging to extract single-neuronal activity from data, because very large background fluctuations and high spatial overlaps intrinsic this recording modality. Here, we describe a new constrained matrix factorization approach accurately separate then demix denoise signals interest. We compared proposed method against previous independent components analysis nonnegative approaches. On both simulated experimental data recorded mice, our substantially improved quality extracted cellular detected more well-isolated neural signals, especially in noisy regimes. These advances can turn significantly enhance statistical power downstream analyses, ultimately improve scientific conclusions derived data.

Language: Английский

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High-dimensional geometry of population responses in visual cortex

Nature, Journal Year: 2019, Volume and Issue: 571(7765), P. 361 - 365

Published: June 26, 2019

Language: Английский

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Reducing Astrocyte Calcium Signaling In Vivo Alters Striatal Microcircuits and Causes Repetitive Behavior

Neuron, Journal Year: 2018, Volume and Issue: 99(6), P. 1170 - 1187.e9

Published: Aug. 30, 2018

Language: Английский

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The Spatiotemporal Organization of the Striatum Encodes Action Space

Neuron, Journal Year: 2017, Volume and Issue: 95(5), P. 1171 - 1180.e7

Published: Aug. 1, 2017

Language: Английский

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The gut–brain axis mediates sugar preference

Nature, Journal Year: 2020, Volume and Issue: 580(7804), P. 511 - 516

Published: April 15, 2020

Language: Английский

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Rational Engineering of XCaMPs, a Multicolor GECI Suite for In Vivo Imaging of Complex Brain Circuit Dynamics

Cell, Journal Year: 2019, Volume and Issue: 177(5), P. 1346 - 1360.e24

Published: May 1, 2019

Language: Английский

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Large-scale two-photon calcium imaging in freely moving mice

Cell, Journal Year: 2022, Volume and Issue: 185(7), P. 1240 - 1256.e30

Published: March 1, 2022

We developed a miniaturized two-photon microscope (MINI2P) for fast, high-resolution, multiplane calcium imaging of over 1,000 neurons at time in freely moving mice. With weight below 3 g and highly flexible connection cable, MINI2P allowed stable with no impediment behavior variety assays compared to untethered, unimplanted animals. The improved cell yield was achieved through optical system design featuring an enlarged field view (FOV) microtunable lens increased z-scanning range speed that allows fast multiple interleaved planes, as well 3D functional imaging. Successive across multiple, adjacent FOVs enabled recordings from more than 10,000 the same animal. Large-scale proof-of-principle data were obtained populations visual cortex, medial entorhinal hippocampus, revealing spatial tuning cells all areas.

Language: Английский

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