MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data

We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: http://sig.biostr.washington.edu/projects/MindSeer webcite.MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine.The problem we address in this report is visualization of integrated multimodality three-dimensional (3-D) brain imaging data. Such visualizations can lead to new insights that are not apparent from a single modality alone.Over the past several years many applications have become available that include some aspect of 3-D visualization. A comprehensive listing of these applications can be found by searching the Harvard Internet Analysis Tools Registry (IATR) [1] for those tools that are indexed by the keyword "visualization". As of March 2007 such a search returned a list of 116 tools. Of these tools many are designed for analysis of specific types of data; as, for example, LORETA for source localized EEG [2]; FSL [3], SPM [4] and AFNI [5] for functional magnetic resonance (fMRI) data; and JAtlasView [6] and the Allen Brain Atlas [7] for gene expression data. Because they are designed for only one type of data these tools generally do not display different types of data at once.On the other end of the spectrum, many tools are general purpose, s