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Web Viewer User Guide

The Allen Brain Explorer (beta) is a browser-based 3D visualization tool to browse multimodal datasets in an annotated 3D spatial framework. The is beta release allows users to explore the Allen Mouse Brain Connectivity Atlas projection data and Allen Reference Atlas (ARA) in a standardized coordinate space.

Launch the browser

Browser Support

The following web browsers have been tested for support:

  • Edge
  • Firefox
  • Chrome
  • Safari

Navigation Controls

All interaction with the tool is via the mouse:

left clickselect a structure or data set
left click + dragrotate the camera
mousewheelzoom in / out
right click + dragpan the camera

View Brain Anatomy

The Web Viewer displays anatomical structures defined as part of the Allen Mouse Common Coordinate Framework.  Briefly, this space is a population average of 1675 P56 mouse brains with 662 structures drawn in 3D. See the technical whitepaper for more details.  

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Anatomical Structure Ontology

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

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Click on the arrow next to a structure to see its sub-structures. You can show 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 name or abbreviation in the search box above the structure ontology.
  • You can make all visible structures partially transparent with the toggle in the header of this box.

Anatomical Annotated Slice Planes

Open coronal, sagittal, and horizontal slice planes by clicking the "toggle slice planes" button. Each plane displays the Common Coordinate Framework's average brain colored to indicate structural boundaries. Drag the colored arrows to move the slice planes.

View Axonal Projections from the Allen Mouse Connectivity Atlas

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 Atlas:

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You can add more experiments to the Web Viewer either by continuing to click links above for different data sets, or by directly typing data set IDs into "Virtual Tractography" box in the Web Viewer itself.

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Once you have one or more projection data sets loaded, you can view primary images from the Connectivity Atlas by clicking either on injection site or projection site voxel objects and opening the "Source Image" panel.

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