MAP: Mouse Atlas Project

Software

IN THIS SECTION:

VIEW ATLAS AND ASSOCIATED SOFTWARE

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

SHIVA (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

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. More Info

SHIVA
BrainGraph
GEMporter
LONI Software