Projection BDA/AAV Comparison Transgenic Characterization Reference Data Brain Explorer Documentation Help
Brain Explorer® 2

The Brain Explorer 2 software is a desktop application for viewing the Allen Mouse Brain Connectivity Atlas projection data and the Allen Mouse Brain Atlas gene expression data in the framework of the Allen Reference Atlas (ARA).

Using the Brain Explorer 2 software, you can:

  • View a fully interactive version of the ARA in 3-D.
  • View projection and gene expression data in 3-D at 200 μm3 resolution.
  • View projection and expression data from multiple image series superimposed on each other in 3-D.
  • Navigate the high-resolution 2-D projection and ISH images using the 3-D model.
  • Link to associated projection and gene metadata in the Allen Mouse Brain Atlas web application.

The 3-D data shown in the Brain Explorer 2 software is generated from the same process employed in the search algorithms on the Allen Mouse Brain Connectivity Atlas web site; see the Brain Explorer paper or the informatics white paper for more information.

After installing the application, you can view projection data by selecting an anatomic structure in the application and searching from the Atlas menu, or you can perform a search from the Projection tab on this website. You can view gene expression data by performing a gene search from the mouse ISH website or from within the application main window. Please see the documentation for more information.

Please verify your system meets the requirements before installing.

Windows Minimum Configuration

  • Operating System: Microsoft Windows 7
  • CPU: Intel Core Duo or AMD 1.8GHz
  • System Memory: 1GB
  • Graphics Card: Hardware 3D OpenGL accelerated AGP or PCI Express with 64MB RAM
  • Screen: 1024x768, 32-bit true color
  • Hard Disk: 200MB free space

Note: Brain Explorer is known to work with the following video chipsets: nVidia GeForce 9400/9600, nVidia Quadro FX 1800/3800/5600, AMD Radeon 9600, AMD Radeon HD 3200/4550, Intel Q35/Q45 Express.

Important: Please install the latest drivers for your video card for best compatibility and performance.

http://support.amd.com/us/gpudownload/Pages/index.aspx
http://www.nvidia.com/content/drivers/drivers.asp
http://www.intel.com/support/graphics/

 

Mac Minimum Configuration

  • Operating System: OS X 10.6.8
  • CPU: Intel 1.8GHz
  • System Memory: 1GB
  • Graphics Card: 3D-capable with 64MB RAM
  • Screen: 1024x768, 32-bit millions of colors
  • Hard Disk: 200MB free space

Note: Please install the latest system updates from Apple to ensure you have the latest video card drivers.