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Rationale and Experimental Overview

The inaugural release of the Allen Brain Observatory aims to elucidate visual coding: How are visual stimuli provides a rich dataset for investigating how visual stimuli are represented by neural activity in the mouse visual cortex in both single cells and populations? To address this question, a . A standardized data acquisition pipeline was established, utilizing two-photon calcium imaging as a means of recording visually evoked responses from animals performing a visual perception task. Primary and secondary areas of the visual cortex in different transgenic mouse lines harboring G-protein coupled calcium-responsive reporters (GCaMP6) in selected cell subpopulations were analyzed , during exposure of to five classical visual stimuli. Ultimately, providing a rich survey of the cells functioning growing dataset to survey information encoding in the visual cortex will be available, as this dataset grows.

Defining visually responsive areas of the cortex

Intrinsic signal imaging (ISI) measures hemodynamic response to sensory stimulation across a wide field of view . ISI and thus was performed used to achieve a "retinotopic map" to represent the spatial relationship of responses stimuli in the visual field to corresponding locations within cortically responsive cortical areas. Retinotopic mapping was used to establish the anatomical boundaries of functionally defined visual areas, and guided targeting of was used to target in vivo two-photon calcium imaging to functionally defined selected locations in primary and secondary visual cortical areas.


Neuronal activity was measured in GCaMP6-expressing neurons from selected cortical layers from transgenic animalspopulations defined by depth and Cre line. For more information on the characteristics of these transgenic lines, see the Transgenic Line Catalog in Documentation.

Video recordings of the visual cortex were gathered during presentation of the various visual stimuli. Activity of the neurons in response to stimuli was detected as transient increases in cellular fluorescence on a millisecond time scale. The data processing of these raw movies involved motion correction and image segmentation to identify the sets of pixels representing distinct cells. The segmentation masks were used to extract traces from each neuron so that cellular activity over time can be quantified, and activity of these identified neurons was extracted as traces for quantification. Ultimately, the activity of each responsive cell may be correlated to the visual stimulus that was viewed by the mouse.