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Visual Coding

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 address this question, 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 five classical visual stimuli. Ultimately, a rich survey of the cells functioning 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 was performed to achieve a "retinotopic map" to represent the spatial relationship of responses in the visual field to corresponding locations within cortically responsive areas. Retinotopic mapping was used to establish functionally defined visual areas, and guided targeting of in vivo two-photon calcium imaging to functionally defined locations in primary and secondary visual cortical areas.

For more information on how ISI was performed and analyzed, refer to the Overview whitepaper in Documentation.

Visual Stimulus and Neuronal Response

Once a standard protocol and equipment were developed, activity of individual neurons to a visual stimulus in a targeted area of the visual cortex could be conducted. Neuronal activity was measured in GCaMP6-expressing neurons from selected cortical layers from four separate transgenic mouse lines. For more information on these how neurons in specific layers and areas were targeted in these transgenic lines, see the Transgenic Line Catalog in Documentation.

Video recordings of the visual cortex were taken during presentation of the various visual stimuli. The data processing of these raw data movies involved motion correction and image segmentation to identify the sets of pixels representing distinct cells. These segmentation masks were used to extract traces from each neuron so that cellular activity over time can be analyzed. The goal was to relate the activity of each cell in the field of view back to the visual stimulus that was viewed by the mouse.

Exploring the data

To learn more about the visual stimulus set as well as the data visualizations that were created to represent the cellular responses, see the visual stimulus pages:

To view the data by experiment, cell list, or individual cell visit the website.

To download the data, visit the Download page.

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