A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

Abstract

SummaryTo understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of neural activity in the awake mouse visual cortex: the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes cortical activity from nearly 60,000 neurons collected from 6 visual areas, 4 layers, and 12 transgenic mouse lines from 221 adult mice, in response to a systematic set of visual stimuli. Using this dataset, we reveal functional differences across these dimensions and show that visual cortical responses are sparse but correlated. Surprisingly, responses to different stimuli are largely independent, e.g. whether a neuron responds to natural scenes provides no information about whether it responds to natural movies or to gratings. We show that these phenomena cannot be explained by standard local filter-based models, but are consistent with multi-layer hierarchical computation, as found in deeper layers of standard convolutional neural networks.

Organization of Neural Population Code in Mouse Visual System

“…Neural activity was monitored through a fluorescent calcium sensor (GCaMP6f) selectively expressed in transgenic mice (de Vries et al, 2018). Recorded calcium signals were processed and discretized in time to yield feature vectors corresponding to neural activity of the population (see Materials and Methods).…”

“…A set of synthetic and natural stimuli, comprised of (1) drifting gratings, (2) static gratings, (3) locally sparse noise, (4) natural images, (5) natural movies, and (6) spontaneous activity (mean luminance gray), were displayed on an ASUS PA248Q LCD monitor at a resolution of 1920 × 1200 pixels (de Vries et al, 2018). Spherical warping was applied to all stimuli to account for the close viewing angle.…”

“…We obtained OSI and DSI using the Allen SDK Drifting Gratings module,$\text{OSI}=\frac{R_{\text{pref}}-R_{\text{orth}}}{R_{\text{pref}}+R_{\text{orth}}}$ $\text{DSI}=\frac{R_{\text{pref}}-R_{\text{null}}}{R_{\text{pref}}+R_{\text{null}}}$where R pref is the mean response to the preferred orientation at the preferred temporal frequency, R orth is the mean response to the orthogonal directions, and R null is the mean response to the opposite direction (Allen Institute for Brain Science, 2017, de Vries et al, 2018). The response was defined as the mean Δ F ∕ F during the grating presentation.…”

Synergistic population encoding and precise coordinated variability across interlaminar ensembles in the early visual system

“…We repeatedly presented a series of fixed-sequence (i.e., repeated) stimuli: a spatially-uniform luminance "flicker" stimulus ( Figure 1Di), which varied in a random but fixed sequence; 118 naturalistic images presented in the same sequence ( Figure 1Dii); and a repeated 30 second naturalistic movie clip (Figure 1Diii, 42 ). Each stimulus was repeated 40-100 times, depending on the recording session.…”

“…The total duration of the luminance flicker was 15 seconds and it was repeated 40-50 times. Naturalistic images (118 total images) were selected from the Berkeley Segmentation Dataset 38 as described elsewhere 42 and were scaled to cover 70º x 70º, beginning 10º into the left visual hemifield and extending mostly in to the right visual hemifield and beginning 15º below the horizon (parallel to mouse platform) and extending into the upper visual field. Images were presented at 10Hz with no inter-image stimulus.…”