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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 at selected cortical depths, 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 imaging locations.

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 this 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 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.

Each experiment in the study is displayed as a row in the Experiment overview page. The columns that uniquely describe an experiment and can be used to sort the data are the "Area", "Driver 1" and "Imaging Depth". The experiments are sorted by the first column and the columns can be moved by clicking and dragging on the column header.

With the inaugural release, all of the columns (minus the two common mouse lines) are displayed by default. Clicking on a row in the "View Cells" or "Experiment" columns will take you to the respective #Cell List or #Experiment Detail Page. Each of the remaining columns displays a visualization summarizing the population response of the neurons in the imaging field of view to the specific visual stimuli. The population thumbnails are shown below and can be explored in more detail from the #Experiment Detail Page.

The population thumbnails are segregated by visual stimulus as indicated by the stimulus color key.

Experiment Detail Page

The experiment detail page presents a more detailed view of all the information for a single experiment. Each experiment is composed of three approximately one-hour imaging sessions.

Imaging Experimental Design

For more information on the visual stimulus set, see the Stimulus Set and Response Analysis whitepaper in Documentation.

Experimental Metadata and Summary Images

Metadata for the experiment is listed at the top of the page including transgenic lines, targeted functional visual areas, imaging depth as well as a link to the #Cell List, which identifies each responding cell in the two-photon calcium imaging sessions. Summary images taken from each of the imaging sessions are included under the metadata.

Population Thumbnails

Below the summary images and metadata are large versions of each of the population thumbnails shown on the #Experiment Overview page, with a description of what the thumbnail represents.

Visual Stimulus



Drifting Gratings

Preferred Direction

Population summary of preferred drift direction of responsive cells


Orientation Selectivity

Cumulative histogram plot indicating the population selectivity for orientation


Direction Selectivity

Cumulative histogram plot indicating the population selectivity for direction


Preferred Temporal Frequency

Histogram plotting the number of cells vs. the temporal frequency (Hz)

Static Grating

Preferred Orientation

Population summary of the preferred orientation of the responding cells


Preferred Spatial Frequency

Histogram plotting the number of cells vs. the spatial frequency (cycles/deg)


Orientation Selectivity

Cumulative histogram plot indicating the population selectivity for orientation


Time to Peak

Temporal dynamics of the mean response time of the responsive cells

Natural Scene

Time to Peak

Temporal dynamics of the mean response time of the responsive cells

Cell List

This page lists all the relevant cells from the selected experiment and shows the cellular responses at a deeper level. Each row represents a single cell and illustrates the cell response through a series of thumbnails that represent a summary of the cellular response to a visual stimuli. Clicking on a row will take you to the #Cell Detail Page.

More information on the development of each of the thumbnails and it's corresponding visual stimulus can be found from the "Visual Stimuli" buttons on the Overview page.

Filtering Cells

To explore the cellular responses within a single experiment, first click on the "Show filters" button at the top left-hand corner of the webpage.

  1. Filters: Show, hide or clear filters by clicking on these buttons
  2. Current Filters: Filters will show in the box once applied
  3. Row Number: The number of cells included in the filter criteria
  4. Filter Criteria: Filters are visual stimulus dependent (static grating, drifting grating, natural scene) and include: Orientation Selectivity (static or drifting gratings), Preferred Orientation (static or drifting gratings), Preferred direction (drifting grating), Preferred phase (static gratings), Preferred spatial frequency (static gratings), Preferred spatial frequency (drifting grating), Time to peak (static grating or natural scene), Preferred image (natural image)

More information can be found on these thumbnails and metrics from the #Cell Detail Page

Cell Detail Page

Information at the level of the individual cell is available from the this page. Similar to the #Experiment Detail Page the top of the page provides metadata from the experiment from which this cell was imaged.

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