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Visual Coding

Rationale

The inaugural release of the Allen Brain Observatory aims to elucidate visual coding: How are visual stimuli represented by neural activity in the mouse visual cortex in both single cells and populations? To answer this question two-photon calcium imaging was recorded from several areas of the visual cortex in four distinct transgenic mouse lines during exposure of five rich visual stimuli.

Creating a Cortical Activity Map

To produce standardized protocols to be able to record from the same cortical area over the extent of the experiment required coordination and hand-off between the many teams performing platform development, data collection and analysis. A basic workflow is outlined below.

Creating a window into the brain

Accurately measuring the activity in a specific visual area in a reproducible and standardized manner first requires a window into the brain - replacing a small section of the skull with a clear glass cover slip that allows visual access to a 5 mm diameter region of the brain.

Being able to consistently locate a cortical region and even a specific cell requires that each system used to collect data maintains a consistent relationship between the mouse's eye and the visual stimulus being presented. To achieve consistent placement of the mouse across systems, and address the challenge of finding and returning to the same cells from day to day, the engineering team designed a custom headframe that is affixed to the mouse’s skull in a standardized location. The headframe consists of a plastic head plate, or well, and a stainless steal clamp-plate that allows repeatable positioning of the animal on each experimental setup. The clamp plate fits perfectly into the placement tool, which in turn is secured to the stereotaxic arm of the surgery rig. Before attaching the head frame, the surgeons use a leveling protocol that is anatomically referenced, so that the headframe is consistently placed over the visual cortex. The cranial window is made within the well to expose the part of the brain that we want to image. This 3D image illustrates the final optimal position of the headframe that ensures we have most or all visual areas accessible within the window.

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