scholarly journals Functional connectomics spanning multiple areas of mouse visual cortex

2021 ◽  
Author(s):  
◽  
Agnes L. Bodor ◽  
Akhilesh Halageri ◽  
Amy Sterling ◽  
Andreas S. Tolias ◽  
...  
Keyword(s):  
Visual Cortex ◽  
Functional Characterization ◽  
Data Access ◽  
Integrated Approach ◽  
Neuron Activity ◽  
Axonal Projections ◽  
Mouse Visual Cortex ◽  
Higher Visual Areas ◽  
Open Access Resource

The value of an integrated approach for understanding the neocortex by combining functional characterization of single neuron activity with the underlying circuit architecture has been understood since the dawn of modern neuroscience. However, in practice, anatomical connectivity and physiology have been studied mostly separately. Following in the footsteps of previous studies that have combined physiology and anatomy in the same tissue, here we present a unique functional connectomics dataset that contains calcium imaging of an estimated 75,000 neurons from primary visual cortex (VISp) and three higher visual areas (VISrl, VISal and VISlm), that were recorded while a mouse viewed natural movies and parametric stimuli. The functional data were co-registered with electron microscopy (EM) data of the same volume which were automatically segmented, reconstructing more than 200,000 cells (neuronal and non-neuronal) and 524 million synapses. Subsequent proofreading of some neurons in this volume yielded reconstructions that include complete dendritic trees as well the local and inter-areal axonal projections. The largest proofread excitatory axon reached a length of 19 mm and formed 1,893 synapses, while the largest inhibitory axon formed 10,081 synapses. Here we release this dataset as an open access resource to the scientific community including a set of analysis tools that allows easy data access, both programmatically and through a web user interface.

scholarly journals A neural circuit for gamma-band coherence across the retinotopic map in mouse visual cortex

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Richard Hakim ◽  
Kiarash Shamardani ◽  
Hillel Adesnik
Keyword(s):  
Visual Cortex ◽  
Neural Circuit ◽  
Brain Slices ◽  
Pyramidal Cells ◽  
Gamma Oscillations ◽  
Gamma Band ◽  
Neuron Activity ◽  
Mouse Visual Cortex ◽  
Retinotopic Map

Cortical gamma oscillations have been implicated in a variety of cognitive, behavioral, and circuit-level phenomena. However, the circuit mechanisms of gamma-band generation and synchronization across cortical space remain uncertain. Using optogenetic patterned illumination in acute brain slices of mouse visual cortex, we define a circuit composed of layer 2/3 (L2/3) pyramidal cells and somatostatin (SOM) interneurons that phase-locks ensembles across the retinotopic map. The network oscillations generated here emerge from non-periodic stimuli, and are stimulus size-dependent, coherent across cortical space, narrow band (30 Hz), and depend on SOM neuron but not parvalbumin (PV) neuron activity; similar to visually induced gamma oscillations observed in vivo. Gamma oscillations generated in separate cortical locations exhibited high coherence as far apart as 850 μm, and lateral gamma entrainment depended on SOM neuron activity. These data identify a circuit that is sufficient to mediate long-range gamma-band coherence in the primary visual cortex.

scholarly journals Canonical and noncanonical features of the mouse visual cortical hierarchy

2020 ◽  
Author(s):  
Rinaldo D. D’Souza ◽  
Quanxin Wang ◽  
Weiqing Ji ◽  
Andrew M. Meier ◽  
Henry Kennedy ◽  
...  
Keyword(s):  
Visual Cortex ◽  
Receptive Field ◽  
Active Vision ◽  
Structural Features ◽  
Hierarchical Organization ◽  
Hierarchical Level ◽  
Continuous Measure ◽  
Axonal Projections ◽  
Visual Cortical ◽  
Mouse Visual Cortex

ABSTRACTNeocortical circuit computations underlying active vision are performed by a distributed network of reciprocally connected, functionally specialized areas. Mouse visual cortex is a dense, hierarchically organized network, comprising subnetworks that form preferentially interconnected processing streams. To determine the detailed layout of the mouse visual hierarchy, laminar patterns formed by interareal axonal projections, originating in each of ten visual areas were analyzed. Reciprocally connected pairs of areas, and shared targets of pairs of source areas, exhibited structural features consistent with a hierarchical organization. Beta regression analyses, which estimated a continuous measure of hierarchical distance, indicated that the network comprises multiple hierarchies embedded within overlapping processing levels. Single unit recordings showed that within each processing stream, receptive field sizes typically increased with increasing hierarchical level; however, ventral stream areas showed overall larger receptive field diameters. Together, the results reveal canonical and noncanonical hierarchical network motifs in mouse visual cortex.

Cloning and functional characterization of the ovine Hormone Sensitive Lipase (HSL) full-length cDNAs: An integrated approach

Gene ◽  
2008 ◽  
Vol 416 (1-2) ◽  
pp. 30-43 ◽  
Author(s):  
Antonis D. Lampidonis ◽  
Alexandros Argyrokastritis ◽  
Dimitrios J. Stravopodis ◽  
Gerassimos E. Voutsinas ◽  
Triantafyllia G. Ntouroupi ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Integrated Approach ◽  
Full Length ◽  
Hormone Sensitive Lipase ◽  
Hormone Sensitive

scholarly journals Maps of cone opsin input to mouse V1 and higher visual areas

2017 ◽  
Vol 117 (4) ◽  
pp. 1674-1682 ◽  
Author(s):  
Issac Rhim ◽  
Gabriela Coello-Reyes ◽  
Hee-Kyoung Ko ◽  
Ian Nauhaus
Keyword(s):  
Visual Cortex ◽  
Mouse Retina ◽  
Dorsoventral Axis ◽  
Intrinsic Signal ◽  
Cone Opsin ◽  
Upper Visual Field ◽  
Wavelength Sensitivity ◽  
Visual Areas ◽  
Mouse Visual Cortex ◽  
Higher Visual Areas

Studies in the mouse retina have characterized the spatial distribution of an anisotropic ganglion cell and photoreceptor mosaic, which provides a solid foundation to study how the cortex pools from afferent parallel color channels. In particular, the mouse’s retinal mosaic exhibits a gradient of wavelength sensitivity along its dorsoventral axis. Cones at the ventral extreme mainly express S opsin, which is sensitive to ultraviolet (UV) wavelengths. Then, moving toward the retina’s dorsal extreme, there is a transition to M-opsin dominance. Here, we tested the hypothesis that the retina’s opsin gradient is recapitulated in cortical visual areas as a functional map of wavelength sensitivity. We first identified visual areas in each mouse by mapping retinotopy with intrinsic signal imaging (ISI). Next, we measured ISI responses to stimuli along different directions of the S- and M-color plane to quantify the magnitude of S and M input to each location of the retinotopic maps in five visual cortical areas (V1, AL, LM, PM, and RL). The results illustrate a significant change in the S:M-opsin input ratio along the axis of vertical retinotopy that is consistent with the gradient along the dorsoventral axis of the retina. In particular, V1 populations encoding the upper visual field responded to S-opsin contrast with 6.1-fold greater amplitude than to M-opsin contrast. V1 neurons encoding lower fields responded with 4.6-fold greater amplitude to M- than S-opsin contrast. The maps in V1 and higher visual areas (HVAs) underscore the significance of a wavelength sensitivity gradient for guiding the mouse’s behavior. NEW & NOTEWORTHY Two elements of this study are particularly novel. For one, it is the first to quantify cone inputs to mouse visual cortex; we have measured cone input in five visual areas. Next, it is the first study to identify a feature map in the mouse visual cortex that is based on well-characterized anisotropy of cones in the retina; we have identified maps of opsin selectivity in five visual areas.

scholarly journals Tracking calcium dynamics from individual neurons in behaving animals

2021 ◽  
Vol 17 (10) ◽  
pp. e1009432
Author(s):  
Thibault Lagache ◽  
Alison Hanson ◽  
Jesús E. Pérez-Ortega ◽  
Adrienne Fairhall ◽  
Rafael Yuste
Keyword(s):  
Visual Cortex ◽  
Calcium Imaging ◽  
Functional Characterization ◽  
Ground Truth ◽  
Time Lapse ◽  
Local Deformation ◽  
Neuron Activity ◽  
Imaging Data ◽  
Wide Range

Measuring the activity of neuronal populations with calcium imaging can capture emergent functional properties of neuronal circuits with single cell resolution. However, the motion of freely behaving animals, together with the intermittent detectability of calcium sensors, can hinder automatic monitoring of neuronal activity and their subsequent functional characterization. We report the development and open-source implementation of a multi-step cellular tracking algorithm (Elastic Motion Correction and Concatenation or EMC2) that compensates for the intermittent disappearance of moving neurons by integrating local deformation information from detectable neurons. We demonstrate the accuracy and versatility of our algorithm using calcium imaging data from two-photon volumetric microscopy in visual cortex of awake mice, and from confocal microscopy in behaving Hydra, which experiences major body deformation during its contractions. We quantify the performance of our algorithm using ground truth manual tracking of neurons, along with synthetic time-lapse sequences, covering a wide range of particle motions and detectability parameters. As a demonstration of the utility of the algorithm, we monitor for several days calcium activity of the same neurons in layer 2/3 of mouse visual cortex in vivo, finding significant turnover within the active neurons across days, with only few neurons that remained active across days. Also, combining automatic tracking of single neuron activity with statistical clustering, we characterize and map neuronal ensembles in behaving Hydra, finding three major non-overlapping ensembles of neurons (CB, RP1 and RP2) whose activity correlates with contractions and elongations. Our results show that the EMC2 algorithm can be used as a robust and versatile platform for neuronal tracking in behaving animals.

scholarly journals Functional characterization of spikelet activity in the primary visual cortex

2015 ◽  
Vol 593 (22) ◽  
pp. 4979-4994 ◽  
Author(s):  
Benjamin Scholl ◽  
Sari Andoni ◽  
Nicholas J. Priebe
Keyword(s):  
Visual Cortex ◽  
Primary Visual Cortex ◽  
Functional Characterization

scholarly journals Classification of electrophysiological and morphological types in mouse visual cortex

2018 ◽  
Author(s):  
Nathan W. Gouwens ◽  
Staci A. Sorensen ◽  
Jim Berg ◽  
Changkyu Lee ◽  
Tim Jarsky ◽  
...  
Keyword(s):  
Visual Cortex ◽  
Laboratory Mouse ◽  
Brain Slices ◽  
Cell Types ◽  
Morphological Properties ◽  
Data Sets ◽  
Multiple Dimensions ◽  
Mouse Visual Cortex

ABSTRACTUnderstanding the diversity of cell types in the brain has been an enduring challenge and requires detailed characterization of individual neurons in multiple dimensions. To profile morpho-electric properties of mammalian neurons systematically, we established a single cell characterization pipeline using standardized patch clamp recordings in brain slices and biocytin-based neuronal reconstructions. We built a publicly-accessible online database, the Allen Cell Types Database, to display these data sets. Intrinsic physiological and morphological properties were measured from over 1,800 neurons from the adult laboratory mouse visual cortex. Quantitative features were used to classify neurons into distinct types using unsupervised methods. We establish a taxonomy of morphologically- and electrophysiologically-defined cell types for this region of cortex with 17 e-types and 35 m-types, as well as an initial correspondence with previously-defined transcriptomic cell types using the same transgenic mouse lines.

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