Allen Brain Explorer (Beta) User Guide

Allen Brain Explorer (beta): User Guide

The Allen Brain Explorer (beta) is a browser-based 3D visualization tool to explore multimodal data in an integrated, anatomically annotated, spatial framework. 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. Future releases will add functionality and additional data. Users are encouraged to provide bug reports or other feedback via Send Us A Message.

Launch the browser

Browser Compatibility

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

  • Edge (HTML 16, Windows 10 Fall 2017 Creator’s Update)
  • Firefox 59
  • Chrome 66
  • Safari 11.1

Browser Navigation Controls

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

Action Behavior
left click select an element: ie, projection path, anatomical structure, experiment, structure or data set
left click + drag rotate the perspective of display
mouse wheel zoom in / out
right click + drag pan the perspective of display

View Brain Anatomy

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

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

Access and visualize brain structures by interacting with the Anatomical Ontology list. This box provides a searchable hierarchical organization of brain structures.

  • 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.
  • Search for structures by typing the name or abbreviation in the text box 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. The default setting is opaque.

View Axonal Projections

The Allen Mouse Brain Connectivity Atlas 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:

When one or more projection data sets are selected, they will be loaded 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 voxels and launching via the Source Image tab in the Experiment Information box. More data sets can be added to the Allen Brain Explorer view either by continuing to select data using the access described above, or by directly typing Experiment IDs into Virtual Tractography box.

Problems? Suggestions? 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.