The software tools bundled with the atlas volumes are SHIVA (visualization and analysis), BrainGraph (navigation and connectivity), and GEMporter (registration and importation).

MBAT (Mouse BIRN Atlasing Toolkit)

Overview of the software (a more complete description of the software) The Mouse Biomedical Informatics Research Network (MBIRN) Atlasing Toolkit (MBAT) is a collaborative effort by groups in the Mouse BIRN to create an interoperable toolkit that offers an intuitive way to access the functionality offered at the various institutions within the Network. The goal of the MBAT is to act as an intuitive, interoperable interface for viewing, accessing, processing, and analyzing multimodal data with emphasis on functionality across distributed locations and diverse databases. This tool allows a user to view their data and offers the ability to interface with data offered by Mouse BIRN. Future plans include the option to incorporate and compare a variety of different data types, regardless of the user’s location or affiliation with the Mouse BIRN.

Synchronized Histological Image Visualization Architecture

(SHIVA) is a platform-independent visualization application, utilizing plug-ins to load and manipulate various 3D image volume file formats. Messages are passed between plug-ins so that the viewers are synchronized, and the data can be compared and manipulated. It has a powerful and flexible message-passing architecture, which allows simultaneous display of multiple image datasets. The architecture seamlessly extends to make every plug-in network-aware, loading data and coordinating viewers over the Internet.


BrainGraph is the hub of the MAP atlas visualization framework. It is a graph-based data model that displays brain structures as a tree based on anatomical containment, providing a simple, intuitive link between image-based and text-based data. As the user traverses the tree, cursor location in the image data is automatically updated and individual nodes can be opened to access more information, such as functional connectivity, anatomical relations to neighbors, developmental information, genetic information, literature references, and other external contextual information.

GEMporter (Gene Expression Map Importer)

GEMporter is a software tool for the registration and importation of user image data into the atlas. It consists of a graphical user interface for priming the image registration and an automated image registration algorithm (AIR) to bring imported data into alignment.

LONI Software

The Laboratory of Neuro Imaging offers software applications, libraries and toolkits for analysis, conversion, processing and visualization of neurological data.