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Table of Contents

Rationale and Experimental Overview

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 address this question, a standardized data acquisition pipeline was established, utilizing two-photon calcium imaging was recorded from several as a means of recording visually evoked responses from animals performing a visual perception task. Primary and secondary areas of the visual cortex in four distinct different transgenic mouse lines harboring G-protein coupled calcium-responsive reporters (GCaMP6) in selected cell subpopulations were analyzed, during exposure of five classical visual stimuli. Ultimately, a rich visual stimulisurvey of the cells functioning in the visual cortex will be available, as this dataset grows.


Defining visually responsive areas of the



Intrinsic signal imaging (ISI) measures the hemodynamic response of the cortex to visual sensory stimulation across the entire a wide field of view. This ISI was performed to achieve a "retinotopic map" effectively represents to represent the spatial relationship of responses in the visual field to corresponding locations within each cortical areacortically responsive areas. Retinotopic mapping was used to delineate establish functionally defined visual area boundariesareas, and enabled guided targeting of the in vivo two-photon calcium imaging to functionally defined locations in primary and secondary visual cortical areas.

Accurately mapping cortical areas involves first imaging the cortical surface with green LED illumination to capture fiduciary markers (vasculature landmarks). Next, imaging of the cortical surface during presentation of a visual stimulus with red LED illumination allows for capture of the hemodynamic response to visual stimuli. For more information on how ISI was analyzed and used to target areas of the cortexperformed and analyzed, refer to the Overview whitepaper in Documentation.