Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Large scale visualization on the Powerwall.
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.


dist-profSCI Institute Director Chris Johnson was recently promoted to the rank of Distinguished Professor of Computer Science. Professor Johnson's research through the years has focused on biomedical computing, visualization, inverse problems and problem solving environments. It is his continuing goal to use his work in scientific computing to create new techniques, tools, and systems, to solve problems affecting various aspects of human life.
For four-year-old Natalie Wright, appearing in front of the state legislature might be just another exciting trip with her family. But, for Governor Mike Leavitt, Natalie represents the fundamental reason for leveraging research and technology within the state of Utah.

Natalie was diagnosed with a brain tumor when she was two years old. Natalie's neurosurgeon knew they had to operate. Natalie's father, John Wright, and neurosurgeon, Dr. Jack Walker called upon the SCI Institute to provide an alternative to conventional technology. Combining years of experience with special techniques in data processing and scientific visualization, Dave Weinstein, Gordon Kindlmann, and Dr. Christopher Johnson created a useful visualization of Natalie's tumor.

scirun-vertThe SCI Institute proudly releases SCIRun version 1.2.0. In direct response to feedback from program users and collaborators, this version contains several new features.

New Features of SCIRun v1.2.0

  • Dynamic Compilation and Loading
  • PETSc SLES support
  • Disjoint package builds
  • Improved Documentation

Dynamic Compilation and Loading

DCL provides dynamic compilation of algorithms in SCIRun which reduces compile-to-experiment time. Often called deferred compilation, the templated C++ code in SCIRun now compiles only when you use it.

darby-jesseTwo SCIers, Darby Brown and Jesse Hall, were given a rare opportunity to showcase their work before the Utah State Legislature on January 18th. In conjunction with a University wide effort to show the benefits of undergraduate studies within a research institution, Darby and Jesse, both undergraduate members of the Scientific Computing and Imaging Institute, along with thirteen other students, made a poster presentation before the newly elected legislature.

“This is a great opportunity for both students and University alike,” says Ronald J.Pugmire. Associate Vice President for Research. “Not only are we given the opportunity to show off our undergraduate programs, but the students are given both the chance to represent their research to their elected officials as well as an early glimpse into the collaboration of education and government.”

uitaOn January 17th Dr. Christopher Johnson, director of the SCI Institute, appealed to local information technology business leaders to assist in lobbying the Utah State Legislature for more funding for Engineering disciplines. Dr. Johnson presented an overview of the current research within the Institute with an emphasis on medicine.

He described the history of biomedical devices from EEG to MRI. The talk also included the story of a real patient treated in part with technology developed here at the SCI Institute. Dr. Johnson described the case of Sarah, a child diagnosed with a tumor near the top of her spinal column. In such cases, doctors are only able to see sets of two-dimensional slices generated from an MRI. The physician must then reconstruct a three-dimensional image from those slices. Using technology developed at the SCI Institute, the team of physicians was not only able to see the tumor in full three-dimensions, but they were also able to use stereo glasses to “virtually” maneuver inside of the MRI. The combination of these technologies gave the surgeons a much clearer visualization and persuaded them to alter how they were going to operate.

leavitt-darbyOn March 19th, Governor Michael Leavitt visited the SCI Institute for a bill signing ceremony that marks the launch of an ambitious initiative to double the number of engineering and technology graduates over the next five years. The law provides funding for new faculty, pay increases, student loans, and infrastructure improvements. Most notably, it provides $15 million in matching funds for the construction of a new engineering building as well as $5 million for remodeling of the current Merrill Engineering Building. The new building will go directly north of the MEB. Gerald Stringfellow, the dean of the U of U College of Engineering, will be challenged to raise an additional $13 million in order to get the funding. Surrounded by students and some of the state's top political leaders, Gov. Leavitt discussed the importance of the new law. “This initiative is an essential step toward accelerating Utah's growth as a technology center,” he said. “It will help employers who face a critical shortage of engineers, and it will provide high-paying jobs for our children.”

map3d-5-2map3d is a scientific visualization application developed at the Nora Eccles Harrison Cardiovascular Research and Training (CVRTI) and the Scientific Computing and Imaging Institute (SCI) at the University of Utah. The original purpose of the program was to interactively view scalar fields of electric potentials from measurements and simulations in cardiac electrophysiology. Its present utility is much broader but continues to focus on viewing three-dimensional distributions of scalar values associated with an underlying geometry consisting of node points joined into surface or volume meshes.

sc2001Dr. Chris Johnson delivered a plenary talk entitled "Scientific Visualization: Bridging the Complexity Threshold" at this year's Supercomputing conference in Denver, Colorado. Dr. Johnson discussed the need to bridge the "complexity threshold" in order to develop useful applications for analyzing data. He reviewed the state-of-the-art in visualization techniques, their use in real world applications, and presented an outline for future visualization research.

Supercomputing 2001 Plenaries
vis-01-best-paperAt the IEEE Visualization 2001 conference in San Diego, Joe Kniss, Gordon Kindlmann, and Chuck Hansen of the SCI Institute were awarded "Best Paper" for "Interactive Volume Rendering with Multi-dimensional Transfer Functions and Direct Manipulation Widgets." This paper focuses on the added value of higher dimensional transfer functions and attempts to solve the complexity of using them with an integrated system. The system features a user interface that joins interactions in both the spatial domain (volume rendering) and transfer function domain, while taking advantage of modern graphics hardware to make it interactive.

bistiThe SCI Institute has been formally awarded a National Institutes of Health grant from the Biomedical Information Science and Technology Initiative(BISTI). This grant will be used to create a Program of Excellence in Computational Bioimaging and Visualization at the University of Utah. The award totals $2,261,136, distributed over three years, and includes collaborators from the departments of Bioengineering, Radiology, Neurosurgery and the Cardiovascular Research and Training Institute (CVRTI). Through awards such as these, NIH Institutes and Centers seek to establish National Programs of Excellence in Biomedical Computing (NPEBC). Funding for the SCI Institute grant comes from the National Heart, Lung, and Blood Institute within the National Institutes of Health.