ISH Data Reference Atlas AGEA Brain Explorer Supplementary Data API Documentation Help About
Brain Explorer
Brain Explorer is a desktop software application for viewing Allen Brain Atlas (ABA) gene expression data in the framework of the Allen Reference Atlas (ARA) in 3D.

Using Brain Explorer, you can:
  • View a fully interactive version of the ARA in 3D
  • View gene expression data in 3D at 100 μm3 resolution
  • View expression data from multiple image series superimposed on each other in 3D
  • Navigate the high-resolution 2D ISH images from the Sleep Study project using the 3D model
  • Link to associated gene metadata on the ABA website
The 3D data shown in Brain Explorer is generated from the same process employed in the search algorithms on the ABA web site; see the the Brain Explorer paper or the Informatics white paper for more information. Download a sample data set, or use one of the following options to download gene expression data directly from the ABA site:
  • Click a gene name in the search results to display a list of image series, then select a 3-D File link
  • In Brain Explorer, use the Search toolbar, or select "Anatomic Search" or "Import Gene List" on the File menu

Please verify your system meets the requirements before installing.

What's New in Version 1.4.2 (July 2008)

  • Compatibility with Windows Vista and Mac OS X 10.5 was improved.
  • The adult mouse brain atlas has moved to http://mouse.brain-map.org. This version of Brain Explorer tracks the new location.

Windows Minimum Configuration

  • Operating System: Microsoft Windows XP or Vista
  • CPU: Pentium 4, Celeron, or Athlon 1.8GHz
  • System Memory: 512MB
  • Graphics Card: 100% OpenGL compliant video card with 32MB video RAM
  • Screen: 1024x768, 32-bit true color
  • Hard Disk: 200MB free space
  • Network Speed: 128 Kbits/sec

Windows Recommended Configuration

  • Operating System: Microsoft Windows XP or Vista
  • CPU: Pentium 4 2.4GHz or AMD 2400xp
  • System Memory: 1GB
  • Graphics Card: 100% OpenGL compliant AGP or PCI Express video card with 64MB RAM
  • Screen: 1280x1024, 32-bit true color
  • Hard Disk: 200MB free space
  • Network Speed: 768 Kbits/sec

Note: Brain Explorer is known to work with the following video chipsets: nVidia GeForce FX, nVidia Quadro FX 1400, nVidia GeForce 6800, ATI Radeon 9000, 9600, 9700, and X1600, and Intel 865G and 915G.

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

http://www.ati.com/
http://www.nvidia.com/content/drivers/drivers.asp
http://www.intel.com/support/graphics/

  

Mac Minimum Configuration

  • Operating System: OS X 10.3.9 or later
  • CPU: G4 1.2GHz or Intel 1.5GHz
  • System Memory: 512MB
  • Graphics Card: 3D-capable with 32MB RAM
  • Screen: 1024x768, 32-bit millions of colors
  • Hard Disk: 200MB free space
  • Network Speed: 128 Kbits/sec

Mac Recommended Configuration

  • Operating System: OS X 10.4.8 or later
  • CPU: G4 1.5GHz or Intel 1.8GHz
  • System Memory: 1GB
  • Graphics Card: 3D-capable with 64MB RAM
  • Screen: 1280x1024, 32-bit millions of colors
  • Hard Disk: 200MB free space
  • Network Speed: 768 Kbits/sec

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