h1. Brain Explorer {reg-tm}{reg-tm} 3-D Viewer


Brain Explorer® is an application for viewing brain anatomy and gene expression data in 3D. It is integrated with three Allen Brain Atlas online resources: the Allen Human Brain Atlas, the Allen Mouse Brain Atlas and the Allen Developing Mouse Brain Atlas.

Using Brain Explorer, you can:

View a fully interactive version of the Allen Mouse Brain Atlas in 3D.
View overlapping expression data from different genes.
Investigate probes or samples of interest in more detail with direct links back to the Allen Mouse Brain Atlas.
Navigate the high-resolution 2D ISH images.

Expression data from the Allen Mouse Brain Atlas can be viewed using Brain Explorer v1.4.

h2. Installation


h3. Windows

For the best performance, please check with your video card vendor  for the latest available drivers before using Brain Explorer. The  Windows version of Brain Explorer is available [here|http://www.brain-map.org/BrainExplorer2/BrainExplorer2.msi]. Double-click the downloaded BrainExplorer2.msi file and follow the prompts.

h3. Mac

The Mac version of Brain Explorer is available [here|http://www.brain-map.org/BrainExplorer2/BrainExplorer2Mac.zip]. Double-click the downloaded zip file to unpack Brain Explorer.

h3. Installing Atlases

A one-time download containing anatomy files is needed following  installation of the Brain Explorer application. The first time you open  Brain Explorer, you will be asked to choose to download files for the  Developing Mouse and Human Brain atlases. Click on the atlases you would  like to use and then click the Install button.

To download missing atlases on the PC, go to the Help menu and select  Download Atlases. On the Mac, the command is in the Brain Explorer 2  menu.

h3. Getting Updates

Brain Explorer will inform you when updates to the Brain Explorer  application itself or its atlases are available. New data may not be  available for viewing until you install the required updates.