The Allen Brain Explorer (beta) is an application that allows users to browse multimodal datasets in an
annotated 3D spatial framework. The most recent release of this application is an integrated web-based
navigator, allowing users to explore the Allen Mouse Brain Connectivity Atlas projection data and Allen
Reference Atlas (ARA) in a standardized coordinate space.
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). This downloadable software will be discontinued in 2019, as improved functionality and new
features will be available via an integrated web-based platform. Ongoing updates to this software will be
discontinued after that time.
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.
The Allen Brain Explorer (beta) is an application that allows users to browse multimodal datasets in an annotated 3D spatial framework. The most recent release of this application is an integrated web-based navigator, allowing users to explore the Allen Mouse Brain Connectivity Atlas projection data and Allen Reference Atlas (ARA) in a standardized coordinate space.
Launch The Allen Brain Explorer (beta)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). This downloadable software will be discontinued in 2019, as improved functionality and new features will be available via an integrated web-based platform. Ongoing updates to this software will be discontinued after that time.
Using the Brain Explorer 2 software, you can:
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.