LONI visualization environment

Abstract

Over the past decade, the use of informatics to solve complex neuroscientific problems has increased dramatically. Many of these research endeavors involve examining large amounts of imaging, behavioral, genetic, neurobiological, and neuropsychiatric data. Superimposing, processing, visualizing, or interpreting such a complex cohort of datasets frequently becomes a challenge. We developed a new software environment that allows investigators to integrate multimodal imaging data, hierarchical brain ontology systems, on-line genetic and phylogenic databases, and 3D virtual data reconstruction models. The Laboratory of Neuro Imaging visualization environment (LONI Viz) consists of the following components: a sectional viewer for imaging data, an interactive 3D display for surface and volume rendering of imaging data, a brain ontology viewer, and an external database query system. The synchronization of all components according to stereotaxic coordinates, region name, hierarchical ontology, and genetic labels is achieved via a comprehensive BrainMapper functionality, which directly maps between position, structure name, database, and functional connectivity information. This environment is freely available, portable, and extensible, and may prove very useful for neurobiologists, neurogenetisists, brain mappers, and for other clinical, pedagogical, and research endeavors.

Fig 1

LONI Viz Sectional Viewer shows cardinal projection planes in the axial, sagittal, and coronal orientation.

Fig 2

BrainGraph is a hyperbolic display of brain ontology systems. Insert in the left shows textual fields saved for each ROI.

Fig 3

3D Surface and Volume Renderer displays surface models, volumetric ROI renderings, and allows oblique sectioning of the virtual scene.

Fig 4

Database Viewer displays externally obtained HTML summaries of homologies, genetics, and anatomical contexts obtained from external databases.

Fig 5

BrainMapper is a synchronizing agent that modulates the communication between the four main components of the LONI Viz environment. It ensures a match between stereotaxic coordinates, region labels, hierarchical representation, and database communication.

Fig 6

LATIS Server provides on-the-fly high-resolution neuroimaging data over HTTP protocols to LONI Viz.

Fig 7

In LayerControls, different color maps are selected to enhance the distinction between the four different imaging modalities simultaneously loaded and superimposed in LONI Viz.

Fig 8

An example of a LONI Viz tool plug-in: semiautomated segmentation of regions of interest using SOCR EM algorithm. Left: The manual region outlining functionality and the resulting superposition of the result of the EM mixture modeling segmentation of the region. Right: Decomposition of the region intensity distribution to a mixture of three Gaussian densities (user has control over the mixture parameters).