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Neuronal Response: Two-Photon Calcium Imaging

The first data modality to be released from the Allen Brain Observatory is a standardized in vivo survey of physiological activity in the mouse visual cortex, featuring representations of visually evoked calcium responses from GCaMP6-expressing neurons in selected cortical layers, visual areas and Cre lines. From the landing page you can view the cre-line, the visual area and the depth of each of the experiments conducted in this survey.

The June 2016 release includes a variety of data visualization summaries capturing visual coding properties of single cell and cell population responses to visual stimuli. Detailed information regarding each of the visual stimuli is available by clicking on the stimulus from the panel below the cortical experiment map.

This resource introduces new cellular visualization summaries distinct for each visual stimulus that describe individual cellular characteristics in a single figure:

Further details on how to interpret these visualizations and how they were created is also available from the "Visual Stimuli" pages.

Access to the experimental data is via the "Data" tab on the menu banner.

Experiment Overview

Every experiment conducted in this study is shown by default on the Experiment Overview page. In the Allen Brain Observatory Visual Coding study, an Experiment is composed of a series of three one-hour long two-photon calcium imaging sessions on an awake mouse exposed to a series of visual stimuli. An experiment is the unique combination of one mouse, one imaging depth (e.g. 175 um from surface of cortex), and one visual area (e.g. “Anterolateral visual area” or “VISal”). More information on the experimental design and the visual stimuli can be found from the whitepapers located in the Documentation.

Targeted Functional Visual Areas



Structure Name



Primary visual area



Lateral visual area



Anterolateral visual area



Posteromedial visual area

*Wang and Burkhalter (J.Comp.Neurol., 502: 339-357. doi: 10.1002/cne.21286)

Transgenic Lines

Two-photon calcium imaging was recorded in neurons expressing a calcium sensitive fluorescent molecule. This is made possible by the use of animals harboring a genetically encoded calcium sensor, GCaMP6, which is imparted by use of the Ai93 line and expressed in subsets of cell populations due to a combinatorial transgenic line breeding strategy. The transgenic lines are a cross of CaMK2a-tTA - a transgene directing tetracycline-controlled transactivator protein (tTA) expression in forebrain excitatory neurons - and one of the following:

  • Cux2-CreERT2
  • Rorb-IRES2-Cre
  • Rbp4-Cre
  • Scnn1a-Tg3-Cre

Further characterization of each of these transgenic lines can be found in the Transgenic Mouse Catalog in Documentation.

Experimental Detail Page

Cell List

Cell Detail Page

Information at the level of the individual cell is available from the Cell Detail Page.

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