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.


mozyAndrew Kensler took the $10,000 grand prize in's Coding Deathmatch. The contest consisted of three timed rounds of competition, two preliminary rounds were held online and the final round at's American Fork (Utah) headquarters. Only the top eight contestants were allowed to proceed to the final round. Contestants were asked to write programs in any of nine possible languages to to solve a series of problems. The winning code was graded on it's ability to solve the problem in the least amount of execution time. The problem for the final round was to write a program that would read through a 2GB file of 20 million records of 100 bytes each. The first 8 bytes represented the key for that record and the remainder was a payload. The program had to write out a file containing just the records that would be in the 0, 1M, 2M, 3M... positions as sorted by the key values. Ties between keys were to be broken by original order in the file. Wall-clock execution time of the correct programs was used to decide the final ranking for the contest. Timings were done on a virtual machine with 1GB of RAM and 4GB of scratch disk space available.

scijumpSCIJump is a computational environment or framework based on the Common Component Architecture (CCA) standard for high performance component frameworks in the scientific computing domain. The SCIJump framework builds on the SCI Institute's SCIRun Problem Solving Environment and implements a parallel component and distributed computation architecture which can support a diverse set of component- based technologies.

nvidiaSCI graduate student Won-Ki Jeong was selected as one of 10 applicants to be awarded the coveted NVIDIA Fellowship Award for 2007-2008. The NVIDIA Fellowship Program provides funding to Ph.D. students who are conducting research on topics which are expected to lead to major advances in the graphics and digital media industry, and are investigating innovative ways of leveraging the power of graphics hardware. Won-Ki Jeong's graduate adviser is SCI faculty member Dr. Ross T. Whitaker.

For more information about the award, please see the NVIDIA press release "NVIDIA Awards Fellowships to Top Ph.D. Innovators."
map3d-6-5The Scientific Computing and Imaging Institute and the Center for Integrative Biomedical Computing are proud to announce the release of map3d version 6.5!

This release includes a number of fixes and additions to the display settings for map3d and major new support for displaying time fiducials. The driving application for this was displaying maps of activation, recovery, start of QRS, etc., both as separate isochronal maps and superimposed on the scalar time series data. If you need this, you will love map3d's new capabilities.

guidoGuido Gerig joins the University of Utah's Scientific Computing and Imaging (SCI) Institute as a USTAR faculty member. The Scientific Computing and Imaging (SCI) Institute has established itself as an international research leader in the areas of scientific computing, scientific visualization, and image processing. USTAR is an innovative, aggressive and far-reaching effort to bolster Utah's economy with high-paying jobs and keep the state vibrant in the Knowledge Age. The USTAR Support Coalition and the Salt Lake Chamber sought public and private investment to recruit world-class research teams in carefully targeted disciplines. These teams will develop products and services that can be commercialized in new businesses and industries.

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(L-R) Dr. Guido Gerig, Dr. Marcel Prastawa, Casey Goodlett, Sylvain Gouttard
The SCI Institute is proud to welcome an Internationally renowned brain imaging team led by Dr. Guido Gerig to our group. Dr. Gerig is a senior researcher in neuroimage analysis from the University of North Carolina at Chapel Hill where he is a Taylor Grandy Professor with joint appointments in the Department of Computer Science and the Department of Psychiatry. At UNC, Dr. Gerig headed the Neuroimage Analysis Laboratory, a multidisciplinary project bringing together experts in Computer Science, Psychiatry, Neurology, Psychology, and Neurosurgery.

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BioPSE network computing the effects of electrode placement on the electrical field in the heart and hence evaluating the defibrillation threshold.
The Scientific Computing and Imaging (SCI) Institute and the Center for Integrative Biomedical Computing (CIBC) are proud to announce the first major release under the new center of their flagship software SCIRun/BioPSE Version 3.0!

The Biomedical Problem Solving Environment, or BioPSE, contains a suite of applications and integrated problem solving systems that have been specialized to meet the needs of scientists working in major fields of biomedicine. In order to design the best systems to meet real world needs, the CIBC has established collaborations with prominent scientists who are leaders in their fields. The goal of these collaborations is to develop software that is well suited to the needs of scientists working in these and related fields of biomedicine.

mozy-deathmatchCompeting individually in the Mozy Code Deathmatch, SCI developers McKay Davis, Michael Callahan and Bryan Worthen represented three of the eight finalists and shared in the grand prize of $10,000. This unique coding contest was conducted with two online preliminary rounds and a final round held at's American Fork (Utah) office. The first round, lasting just an hour, required contestants to solve six small programming puzzles. The second round challenged the remaining contestants with four more difficult problems. The eight finalists then were invited to's office to compete head-to-head. In the final round, the contestants were asked to write - in under ninety minutes - a small web server capable of handling 10,000 simultaneous connections. To assess the contestants' efforts, the judges then used a test client to connect and to establish a data connection with each server 10,000 times in a short period. Each server then had to sort the data and retrieve three specific pieces of the data. Although all finalists managed to develop a functioning server, none of their servers scaled well enough to meet the full scope of the challenge. After some debate, all agreed to declare the competition a tie and to split the prize money equally among the finalists.

scidacThe SCI Institute is pleased to announce that it will be participating in three DOE SciDAC 2 research centers.

The Visualization and Analytics Center for Enabling Technologies (VACET), includes SCI Institute faculty Chris Johnson (Center Co- PI with Wes Bethel from LBNL), Chuck Hansen, Steve Parker, Claudio Silva, Allen Sanderson and Xavier Tricoche. The center will focus on leveraging scientific visualization and analytics technology to increase scientific productivity and insight. It will be challenged with resolving one of the primary bottlenecks in contemporary science, making the massive amounts of data now available to scientists accessible and understandable. Advances in computational technology have resulted in an "information Big Bang," vastly increasing the amount of scientific data available, but also creating a significant challenge to reveal the structures, relationships, and anomalies hidden within the data. The VACET Center will respond to that challenge by adapting, extending, creating when necessary, and deploying visualization and data understanding technologies for the scientific community.

shephardSCI graduate student Jason F. Shepherd and coauthor Carlos D. Carbonera have published a solution to Problem #27 of The Open Problems Project's list of unresolved problems in computational geometry. The question is:
Can the interior of every simply connected polyhedron whose surface is meshed by an even number of quadrilaterals be partitioned into a hexahedral mesh compatible with the surface meshing?
The solution of Carbonera and Shepherd settles the practical aspects of the problem by demonstrating an explicit algorithm that extends a quadrilateral surface mesh to a hexahedral mesh where all the hexahedra have straight segment edges. This work did leave one aspect of the problem open. The authors did not resolve the question of achieving a hexahedral mesh with all planar faces. The collaborators are now working on a revision that should close this problem definitively.

C. D. Carbonera, J.F. Shepherd, "A Constructive Approach to Constrained Hexahedral Mesh Generation," Proceedings, 15th International Meshing Roundtable, Birmingham, AL, September 2006.

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