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.