Overview: Allen Brain Observatory

Visual Coding

Rationale and Experimental Overview

The Allen Brain Observatory 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. 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 to five classical visual stimuli, providing a growing dataset to survey information encoding in the visual cortex.

Defining visually responsive areas of the cortex

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

Neuronal activity was measured in GCaMP6-expressing neurons from selected populations 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, 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.

Availability of 2-photon calcium fluorescence movies

Motion-corrected 2-photon calcium fluorescence movies are too large to download conventionally, but are available upon request. Each experiment contains three movie files of approximately 60 GB each. We ask that anyone requesting movies provide one or more hard drives with sufficient capacity to store the files and a shipping number from your organization for return. These will be returned after file transfer is complete. Data is provided under the Allen Institute Terms of Use policy.

To request movie files, please contact us to indicate:

  • desired movies from specific experiments
  • point of contact name and email address
  • organization
  • area of research
  • proposed use of the data

Upon receipt of this message, arrangements will be made with the point of contact and will usually be complete within two weeks of the receipt of a storage drive.

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 characterization of the transgenic mouse lines used in this study, see the Transgenic Characterization tab.

To view the data by experiment click on the Experiments tab.

To search the experiments for cells with certain response criteria, click the Cells tab.

To download the data, visit the Download page.