Date of Graduation


Document Type


Degree Type



Statler College of Engineering and Mineral Resources


Lane Department of Computer Science and Electrical Engineering

Committee Chair

Gianfranco Doretto

Committee Co-Chair

Yenumula V. Reddy

Committee Member

George A. Spirou


The complex nature of neuronal cellular and circuit structure poses challenges for understanding tissue organization. New techniques in electron microscopy allow for large datasets to be acquired from serial sections of neuronal tissue. These techniques reveal all cells in an unbiased fashion, so their segmentation produces complex structures that must be inspected and analyzed. Although several software packages provide 3D representations of these structures, they are limited to monoscopic projection, and are tailored to the visualization of generic 3D data. On the other hand, stereoscopic display has been shown to improve the immersive experience, with significant gains in understanding spatial relationships and identifying important features. To leverage those benefits, we have developed a 3D immersive virtual reality data display system that besides presenting data visually allows augmenting and interacting with them in a form that facilitates human analysis.;To achieve a useful system for neuroscientists, we have developed the BrainTrek system, which is a suite of software applications suited for the organization, rendering, visualization, and modification of neuron model scenes. A middle cost point CAVE system provides high vertex count rendering of an immersive 3D environment. A standard head- and wand-tracking allows movement control and modification of the scene via the on-screen, 3D menu, while a tablet touch screen provides multiple navigation modes and a 2D menu. Graphic optimization provides theoretically limitless volumes to be presented and an on-screen mini-map allows users to quickly orientate themselves. A custom voice note-taking mechanism has been installed, allowing scenes to be described and revisited. Finally, ray-casting support allows numerous analytical features, including 3D distance and volume measurements, computation and presentation of statistics, and point-and-click retrieval and presentation of raw electron microscopy data. The extension of this system to the Unity3D platform provides a low-cost alternative to the CAVE. This allows users to visualize, explore, and annotate 3D cellular data in multiple platforms and modalities, ranging from different operating systems, different hardware platforms (e.g., tablets, PCs, or stereo head-mounted displays), to operating in an online or off-line fashion. Such approach has the potential to not only address visualization and analysis needs of neuroscientists, but also to become a tool for educational purposes, as well as for crowdsourcing upcoming needs for sheer amounts of neuronal data annotation.