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Web Viewer User Guide

The Allen Brain Explorer (beta) is a browser-based 3D visualization tool to browse to explore multimodal datasets data in an an integrated, anatomically annotated 3D , spatial framework. The is beta  This initial release allows users to explore the Allen Mouse Brain Connectivity Atlas projection data and Allen Reference Atlas (ARA) in a standardized coordinate space. Users are encouraged to provide bug reports or other feedback via Send Us A Message.

Launch the browser




The following web browsers have been tested for support, using updated versions as of June 2018:

  • Edge
  • Firefox
  • Chrome
  • Safari


Browser Navigation Controls

All interaction with the tool is via the mouse:


At this time, this application supports use of a clickable mouse for selecting and interacting with data.

left clickselect an element: ie, projection path, anatomical structure, experiment, structure or data set
left click + dragrotate the cameramousewheelperspective of display
mouse wheelzoom in / out
right click + dragpan the cameraperspective of display

View Brain Anatomy

The Web Viewer Allen Brain Explorer displays anatomical structures defined as part of in the Allen Mouse Common Coordinate Framework.  Briefly, this space is created using a population average of 1675 P56 1,675 C57/Bl6 adult mouse brains, with 662 structures drawn annotated structures rendered in 3D. See the  Refer to the technical whitepaper for more details on creation and annotation of this reference atlas and spatial framework.  

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Navigation Tools: 


Anatomical Annotated Reference Planes and Grid

Open coronal, sagittal, and horizontal slice planes by clicking the Toggle Reference Planes button. Each plane displays the structural boundaries of the annotated brain areas. Drag the colored arrows to move the slice planes.  A grid can be toggled to provide approximate spatial scale.  Future releases will include accurate scale information.

Anatomical Structure Ontology

Download and visualize 3D anatomical Access and visualize brain structures by interacting with the anatomical structure ontology Anatomical Ontology list. This box shows box provides a hierarchical searchable hierarchical organization of brain structures annotated in the Allen Mouse Common Coordinate Framework


  • Click on the


  • white arrowhead next to a structure


  • to view its sub-structures.


  • Display or hide the 3D representation of a particular structure by clicking the "eye" icon next to the structure.

Other actions you can take from the structure ontology box:

  • Search for structures by typing the name or abbreviation in the search the text box above the structure ontology.You can make all visible structures partially transparent with the toggle next to the magnifying glass icon.
  • View anatomical structures with opaque or semi-transparent color schemes using the toggle slider in the header of this box.

Anatomical Annotated Reference Planes


  •   The default setting is opaque.

View Axonal Projections


The Allen Mouse Brain Connectivity Atlas provides links to open the Web Viewer and visualize approximate projection pathways for a data set of interest. You can open the 3D viewer from three places in the AtlasAtlas contains icons to access data via this Allen Brain Explorer viewer.  Users can visualize anatomically mapped projection pathways, and explore more detailed experimental information, including image data. The Allen Brain Explorer can be accessed from three other sources throughout the Allen Mouse Brain Connectivity Atlas, using the icons highlighted in red below:

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Once you have When one or more projection data sets are selected, they will be loaded , you can view primary images from the Connectivity Atlas into the Allen Brain Explorer, and displayed in the Virtual Tractography box.  Primary data images can then be viewed by clicking either on injection site or projection site voxel objects and opening voxels and launching the "Source Image" paneltab. You can add more experiments to the Web Viewer  More data sets can be added to the Allen Brain Explorer view either by continuing to click links above for different data setsselect data using the access described above, or by directly typing data set Experiment IDs into "Virtual Tractography" box in the Web Viewer itself.Image Removed box.

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Problems?  Questions?  Users are encouraged to provide bug reports or other feedback via Send Us A Message, located in the lower right of the Allen Brain Explorer, or in the footer of other pages of the Allen Brain Atlas portal. Include reference to the Allen Brain Explorer in your message.