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Allen Brain Observatory: Visual Coding
The Allen Brain Observatory presents its inaugural dataset, allowing for quantitative exploration of the functional properties that underlie coding of sensory stimuli through the visual pathway, at both the single-cell and population levels. The characterization of visually evoked cellular responses is carried out using in vivo calcium imaging from GCaMP6-expressing neurons measured from selected brain areas, cortical layers, and Cre lines. The cellular responses acquired during the presentation of the Locally Sparse Noise stimulus provide data to help characterize visual tuning properties of cells, such as definition of the spatial receptive field, including both On and Off subunits.
Visual Stimulus: Locally Sparse Noise
Conventionally, the spatial dimensions of the receptive field have been measured with a sparse noise stimulus, which consists of a mean luminance gray display with a single white or black spot presented briefly in different locations. This stimulus allows the visual field to be fully sampled with both light (On) and dark (Off) stimuli to map the extent of the cells' receptive fields. Complete sampling of all positions in the visual field can require hours of visual stimulus data collection.
Sparse noise
White spot is "On" stimulus, black spot is "Off" stimulus
To examine the spatial extent of the receptive fields in an efficient manner, a "Locally Sparse Noise" stimulus was developed. In this display, multiple black and white spots are presented in each stimulus frame (250 ms each). Each spot is 4° on a side, and is surrounded by a spatial exclusion zone of 20° that is not occupied by any other spot. This reduces the amount of time that is needed to quantify cell responses in the visual field.
Locally sparse noise
Evaluating cellular responses to the Locally Sparse Noise visual stimulus
To map the receptive field structure, the cellular response is averaged over all trials (~115 trials) when a given location is occupied by a spot, (i.e., a white spot). While there were other spots present in the stimulus for this particular trial, the arrangement of these spots was always different, such that the effect of the other spots on a cell's response should average away. A heatmap of a cell's On responses is created by looking at these average responses for each location in the visual field. Similarly, a heatmap of the cell's Off responses can be created by looking at the responses for the black spots across all locations.
Evaluating cellular responses to the Locally Sparse Noise visual stimulus: Simplifying data display
Consistent with the other visualizations in the Allen Brain Observatory, a figure highlighting the trial-to-trial variability of the responses to this stimulus, or the "Pincushion" plot, was created. For each location in visual space, all of the trials for an On stimulus are ranked and represented as dots, whose red hue corresponds to the strength of that trial. The same is done for the “off” stimulus in blue plots. This visualization not only shows the locations of strong responses to the On and Off stimuli (e.g. the On and Off subunits), but also reveals where the presence of the On or Off stimulus causes a suppression of activity, evidenced by a smaller number of red or blue dots than in surrounding areas.

"On" pincushion plot

"Off" pincushion plot