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Adult Mouse Brain Reference Atlas

One of the primary goals of the Allen Mouse Brain Atlas is to create a cellular-resolution, genome-wide map of gene expression in the mouse brain. To complement gene expression data, a mouse reference atlas was created by Hong Wei Dong, M.D., Ph.D., in the coronal and the sagittal plane. The reference atlases are full-color, high-resolution, Web-based digital brain atlases accompanied by a systematic, hierarchically organized taxonomy of mouse brain structures. The gene expression data and reference atlases are derived using identical methodology, from 8-week old C57Bl/6J male mouse brains prepared as unfixed, fresh-frozen tissue.

The Allen Reference Atlas was designed to:

  • Allow users to directly compare gene expression patterns to neuroanatomical structures.
  • Serve as templates for the development of 3-D computer graphic models of mouse brain, providing a foundation for the development of informatics-based annotation tools.
  • Provide a standard neuroanatomical ontology for determining structural annotation and aid in the construction of a detailed searchable gene expression database.

The coronal reference atlas consists of 132 coronal sections evenly spaced at 100 µm intervals and annotated to a detail of numerous brain structures. The sagittal reference atlas consists of 21 representative sagittal sections spaced at 200 µm intervals, annotated for 71 major brain regions.

The Allen Reference Atlas was first released online in 2005, and underwent several updates to add increasing complexity to the neuroanatomic delineations. Version 1 (2008) is used on the website to refer to the version of the atlas that was completed for publication as the print atlas (Dong, 2008) and used as the primary reference atlas in the Allen Mouse Brain Atlas until November 2011. Since that time, Version 2 (2011) has been developed to enable interactive exploration of the atlas online.

From the Reference Atlas landing page in the Allen Mouse Brain Atlas, you can explore the atlases in the Interactive Atlas Viewer or you can view the static 2008 versions of the images.

Interactive Atlas Viewer (IAV)

The Interactive Atlas Viewer (IAV) is a valuable tool for exploring the anatomy of the mouse brain and providing a context for the experimental images from the Allen Mouse Brain Atlas.

Accessing the Interactive Atlas Viewer

Access to the IAV is from the button on the Data Portal, the "key" icon from the Reference Atlas Zoom and Pan (ZAP) Image Viewer when viewing experiments in the experiment image viewer, or from the High Resolution Image Viewer.

Using the Interactive Atlas Viewer

The IAV is a stand alone application that can be used to explore adult mouse neuroanatomy. It can also be utilized in the High Resolution Image Viewer to visualize the reference atlas side by side with and ISH image series. To use in this manner, please click here.

Features of the Interactive Atlas Viewer

  1. Structure Search - Search by typing a structure name or abbreviation and choose from a list of suggestions from the Structure Hierarchy.
  2. Structure Hierarchy - please see the Reference Atlas (2011) whitepaper in the Documentation tab for more information.
  3. Main Image Viewer - A Zoom and Pan (ZAP) Image Viewer showing the thumbnail section outlined in blue below the image.
  4. On-screen Navigation Bar - Mouse operated navigation buttons that allow for zooming, panning and moving through the thumbnail images. Also indicates the image section number as well as the zoom parameters.
  5. Structure Metadata - Indicates the current atlas view, and shows the name and abbreviation of the structure the mouse is currently hovering over.
  6. Atlas/Neuroanatomic Guide Selection Menu - A drop-down menu that allows you to choose from each of the atlases or guides available via the IAV.
  7. Alternative Background Images - A drop-down menu that allows you to choose between the Atlas (default) or the Nissl images as a background view.
  8. Settings Menu - A drop-down menu that allows you to toggle views in the image viewer (Metadata, annotations) as well as download images.

Structure Hierarchy

The anatomical structures are listed in a hierarchical tree in the left-hand pane of the viewer. The tree can be expanded and collapsed to browse to a structure of interest. Clicking on any structure will highlight that structure in the image viewer to the right.

A search function is available to find any structure in the list by typing in part of the name or acronym of the structure. Structures in the list labeled with a black font have a corresponding structure in the atlas. Structures listed in medium gray have at least one descendent with an annotated structure. Those structures listed in a light gray italic font do not have an annotated structure in the atlas.

Image viewer

The right-hand pane of the interactive atlas viewer displays the images of the reference brains in a Zoom and Pan (ZAP) Image Viewer. Thumbnail images of each section of the reference atlas line the lower border of the pane; click on any one to view it in the main viewing window.

Images in the main viewer are annotated with polygons hand drawn by Allen Institute neuroanatomists. The polygons will scale and move with the image as the user zooms in and out or moves the image in any direction. Moving the computer cursor over the image will highlight individual structures; the name and acronym of the structure in the Allen Reference Atlas will be displayed at the top of the window. Clicking on a structure will also highlight the structure in the hierarchy of the left-hand pane. In the coronal reference atlas, only one of the hemispheres is annotated.

Drop-Down Menus

Selection Menu

From this menu, you have access to any of the Allen Brain References Atlases. When a structure is selected, moving to another atlas that uses the same ontology, will open that atlas at the same selected structure. Conversely, atlases that use different ontologies (i.e adult mouse vs. developing mouse) will not synch to the same location.

Alternative Background Images

From this menu, you can overlay the annotations over the Nissl image series used to draw the structure polygons.




The Settings menu allow you to change the settings of the image viewer. From this menu you can download individual images and toggle features such the Atlas or structure metadata, thumbnail image viewing or the various annotations.

Zoom And Pan (ZAP) Image Viewer

The Zoom and Pan (ZAP) Image Viewer is a powerful tool to navigate and view the images in an experiment. The main part of the viewer is an interactive window where an image can be repositioned by dragging with a mouse. Use the scroll wheel or the keyboard to zoom in or out.

Scale Bar

Drag the scale bar with your mouse to the desired location. Click the text with your mouse to toggle between horizontal and vertical.

Keyboard Commands

Use the keyboard to navigate through the image series. Keyboard commands include:




Advance to the next image in the series


Go back to the previous image in the series


Advance to the last image in the series


Go back to the first image in the series


Zoom in


Zoom out


Zoom in. Please note that some keyboards may require the [Shift] key be held down while pressing the [+] key


Zoom out

You can also use the arrow keys to pan the current image.

Using The High Resolution Image Viewer

The Interactive Atlas Viewer has been incorporated into the High Resolution Image Viewer, which is used to look at experimental ISH images in higher resolution.

When viewing an ISH image series either in a gene detail page view or in an experimental image viewer, you can open a High Resolution Image Viewer by clicking on the icon.

Interacting with the High Resolution Image Viewer is similar to using the ZAP Viewer with some enhanced features accessible from icons in the top right hand of the main image viewer.



View ISH, Expression Energy, or Reference Stain (Nissl or Feulgen-HP Yellow)

View experiment side by side with the Interactive Reference Atlas

Allows you to access setting options, including downloading the current image

Side-By-Side Reference Atlas Viewing

To open up the reference atlas in a side-by-side view, click the icon.

In this view, other options become available at the top of the image viewers



Choose between the drawn images or the Nissl stains in the background

Syncs the other image to the current windows section, zoom and pan

Opens the Ontology Hierarchy

Clicking the Ontology Hierarchy button will open the Ontology in the Atlas window.

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