Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.
Dr. Xavier Tricoche

Computational Fluid Dynamics (CFD) has become an essential tool in various engineering fields. In aeronautics it is a key element in the design of modern aircrafts. The performances of today's computers combined with the increasing complexity of physical models yields numerical simulations that accurately reproduce the flow structures observed in practical experiments and permit to study their impact on flight stability. Yet, to fully exploit the huge amount of information contained in typical data sets engineers require powerful post-processing techniques that allow insight into the results of their large-scale computation.

Flow visualization aims at addressing this challenge by offering intuitive and effective depictions of interesting flow patterns. Unfortunately, many problems remain that limit the usefulness of existing methods in practical applications. Our recent work has focused on the design of new visualization techniques suitable for large-scale CFD simulations. Special emphasis was put on critical flight situations that lead to turbulent and vortical flows as well as complex and structurally involved phenomena like flow recirculation and vortex breakdown.

Yarden Livnat, Xavier Tricoche

We have proposed a novel point-based approach to view dependent isosurface extraction. We also introduce a fast visibility query system for the view dependent traversal, which exhibits moderate memory requirements. Using this technique, we achieved an interactive interrogation of the full visible woman dataset (1GB) at more then four frames per second on a desktop computer. The point-based approach is based on an extraction scheme that classifies different sections of the isosurface into four categories. The classification is based on the size of the geometry when projected onto the screen. In particular, we use points to represent small and sub-pixel triangles, as well as large sections of the isosurface whose projection has sub-pixel size. An important issue raised by point-based processing is how to assign a normal to an isolated point representing a large, but far, section of the isosurface. We propose to define such normals during a post processing of the extracted isosurface and provide the corresponding hardware implementation.

isosurface fig1 Figure 1: Left: A section of the visible female skeleton. Middle: A closeup view of the extracted points. Right: The final visibility mask. The color represent different levels of the mask hierarchy

Jennifer Simpson, Eric luke, MS., Allen Sanderson, Phd.


In the last few years, scientists and researchers have given a great deal of attention to the area of remote visualization of scientific datasets within collaborative environments. This recent interest has been fueled by the use of interactive viewing as the primary means by which researchers explore large datasets. However, researchers often need to extend this interactivity in order to collaborate with colleagues who are geographically separated. Most current remote visualization tools allow multiple parties to view images from different locations, but pose problems with efficiency and user interactivity.

Undergraduate research opportunities at the University of Utah have dramatically increased in the past several years. Positions that were once reserved for graduate students have now been opened up through a variety of programs. The SCI Institute has taken full interest in promoting and co-sponsoring these opportunities--namely, the Engineering Scholars Program and the Access Program for Women in Science and Mathematics, both of which offer scholarships to first year undergraduates and present them with the opportunity to work side-by-side with professors and researchers in various labs.

Michelangelo's David; a large-scale seismic volume; the moons of Jupiter; four half-full wine glasses; the Greek Parthenon. What do these models have in common? They were all part of the Star-Ray demonstration at SIGGRAPH 2002, held in San Antonio, July 22-24. With support from SGI, researchers from SCI, GDC, VisSim, and the Graphics group designed, implemented, and premiered interactive ray-tracing of a complex virtual underwater world for thousands of graphics enthusiasts at the world's premier computer graphics conference.

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star-ray galaxy star-ray atlantis  
(left to right) Living Room Scene, Graphics Museum, Science Room, Galaxy Room, Atlantis Scene

A. Samsonov, R. Whitaker, C.R. Johnson

Intensity inhomogeneity is one of the main obstacles for MRI data post processing. The problem requires retrospective correction due to the strong dependence of the inhomogeneity on patient anatomy and the accompanying acquisition protocol. We have developed a new method for correcting the inhomogeneities using a polynomial estimation of the bias field. The method minimizes the composite energy function to find parameters of the polynomial model. The energy function is designed to provide a robust estimation of the bias field by combining measures from histogram analysis and local gradient estimation. The method was validated on a wide range of MRI data obtained with coils of different types and under different acquisition protocols.

The developed method provides reliable estimation of the intensity inhomogeneities in MRI data. The correction times are dependant on the number of parameters the model used, the dataset size and the degree of subsampling in estimation of both local and global terms and vary from 1 to 5 minutes using a mid range PC.

Dr. Ross Whitaker and Vidya Elangovan

dendrite yellowTraditionally, processing tomographic data begins with reconstructing volumes. However, when the tomographic data is incomplete, noisy, or misregistered tomographic reconstruction can produce artifacts in the volume, which makes subsequent segmentation and visualization more difficult. Researchers in the SCI institute are developing direct methods for segmenting tomographic data. The strategy is to fit 3D surface models directly to the tomographic projects, rather than the volume reconstructions. In this way, the surface fitting is not influenced by reconstruction artifacts. Implementing this strategy requires several technical advances. First is a mathematical formulation that relates object shape directly to tomographic projections. This results in a description of how surfaces should deform in order to match the tomographic data. The second advance is the use of a surface modeling technology that can accommodate a wide variety of shapes and support incremental deformations. This is done using 3D level-set models, which results in a 3D partial differential equation (PDE). The final advance is development of computational schemes that allow us to solve these PDE's efficiently. For these we have developed the incremental projection method which significantly reduces the amount of computation needed to deform these 3D surface models.

J.D. Brederson and M. Ikits

What is Immersive Visualization?

The goal of visualization is to aid in the understanding of complex scientific data, typically using techniques from the fields of computer graphics and animation. To gain additional insight, immersive visualization places the user directly within the data space through virtual reality technology. The resulting immersive experience allows exploration from a first-person perspective, in contrast to the third-person interaction typical of desktop environments.

The feeling of actually "being there" in a virtual environment, also known as presence, is created by fooling one or more of the user's senses with computer generated cues. In a typical system, stereo images provide a sense of visual depth and natural interaction is achieved with tracking sensors and 3D input devices. More advanced systems may also include force-feedback, spatialized audio, and/or voice recognition capabilities to increase the sense of presence.

Imagine directly navigating through a scientific dataset, much like one experiences the real world. How would it feel to investigate the interesting features of the data with your sense of touch? Would this capability be useful or not? These are the types of questions Virtual Reality (VR) researchers at the SCI institute currently seek to answer.

By J. Kniss, G. Kindlmann, C. Hansen

This page documents the evolution of our volume rendering project, named Simian. As volume rendering goes, this system is quite a departure from the way this process is typically approached. Most direct volume renderings produced today employ one-dimensional transfer functions, which assign color and opacity to the volume based solely on the single scalar quantity that comprises the dataset. Multi-dimensional transfer functions, however, are an effective way to extract specific material boundaries and convey subtle surface properties. However, finding good transfer functions is hard enough in one dimension, let alone two or three.

Lisa Durbeck

Part 1. Unstructured Meshes in Entertainment and Engineering

TombRaider TombRaider3
Tomb Raider

If you have played just about any modern Nintendo(tm) or Playstation (tm) computer game, then you have encountered meshes. Many games make heavy use of what are called polygonal surface meshes, or surfaces built up out of polygons. They are used in the models of many of the people and cars and other 3D things within the game. Polygonal models are a good way for the game designers to get what they want out of the hardware inside the computer or whatever you are using to play the game. I'll explain what a mesh actually is, how it is constructed, and how engineers use meshes to solve problems.

By Gordon Kindlmann.

fancydotsThe technology of Magnetic Resonance Imaging (MRI) has been used in an ever-increasing variety of applications in the area of medical imaging. This is partly because of MRI's basic ability to non-invasively and non-destructively take images of living tissue, and also because of the inherent flexibility in the way that MRI machines are programmed in order to acquire images. One relatively new method of using MRI technology is called "diffusion tensor imaging". By measuring the directions along which water molecules diffuse through brain tissue, this technology allows us to explore the structure of the brain in new ways which benefit many disciplines. For example, it can help doctors to better detect abnormalities in brain tissue, cognitive scientists to better understand the interconnections between the functional units of the brain, and show biologists how brain tissue becomes organized in a growing fetus.