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.

News

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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 Mozy.com'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 Mozy.com'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.


Versions Available: [PDF]
sarangDr. Sarang Joshi has joined SCI as an Associate Professor of the Department of Bio Engineering. Before coming to Utah, Dr. Joshi was an Assistant Professor of Radiation Oncology and an Adjunct Assistant Professor of Computer Science at the University of North Carolina in Chapel Hill. Prior to joining Chapel Hill, Dr. Joshi was Director of Technology Development at IntellX, a Medical Imaging start-up company which was later acquired by Medtronic. Sarang's research interests are in the emerging field of Computational Anatomy and have recently focused on its application to Radiation Oncology. Most recently he spent a year on sabbatical at DKFZ (German Cancer Research Center) in Heidelberg, Germany, as a visiting scientist in the Department of Medical Physics where he focused on developing four dimensional radiation therapy approaches for improved treatment of Prostate and Lung Cancer.

Dr. Joshi received his D.Sc. in Electrical Engineering from Washington University in St. Louis. His research interests include Image Understanding, Computer Vision and Shape Analysis. He holds numerous patents in the area of image registration and has over 50 scholarly publications.
corbatoSteve Corbató has joined the University of Utah's Scientific Computing and Imaging (SCI) Institute as its Associate Director. The Scientific Computing and Imaging (SCI) Institute has established itself as an international research leader in the areas of scientific computing, scientific visualization, and imaging, and in this new position Steve will help lead more than 100 faculty, staff and students in pursuing innovative, ground-breaking research and development aimed at solving important problems in science, engineering, and medicine.

Steve most recently served as Managing Director for Technology Direction and Development at Internet2, a non-profit, university-led consortium focused on developing and deploying advanced Internet technologies. In that role, he oversaw a broad portfolio of initiatives in high-performance networking, middleware, network diagnostics, and security. He also worked to develop overall strategy and key relationships for Internet2's next generation of network infrastructure.

Dr. Claudio Silvaclaudio has been honored once again with a coveted IBM Faculty Award. This award is designed to promote innovative, collaborative research and honor outstanding faculty working in disciplines of interest to IBM. Dr. Silva is being recognized for his work developing efficient rendering techniques for large-scale scientific visualization. Much of modern science and engineering occurs on a computer, analyzing data collected from a variety of sources. Often the size of the datasets under analysis overwhelms the processing ability of whatever computer resources are available. Usually, in order to visualize a dataset it is necessary to have the entire dataset in main memory at once. Dr. Silva's project is developing faster, more efficient algorithms for processing large data and methods for dynamically loading only those parts of the data immediately needed for visualization. These methods show great promise for significantly improving our ability to visualize large datasets.

This award includes $30,000 to support ongoing research. This is the second year in a row IBM has chosen to honor Dr. Silva with this award.
parkerParker, Steve
Research Assistant Professor
University of Utah

"The impact of high-performance computing on society has been astounding, but I believe that we are just starting to see the tip of the iceberg. HPC is going to play an integral role in tackling many of the world's toughest scientific challenges as we continue through the 21st century, and will shape our national policy, our laws, and even our health."
- Steve Parker


Why he's worth watching: As Research Assistant Professor at the University of Utah, Steve Parker specializes in HPC environments, focusing on tackling the toughest multi-scale, multi-physics computational challenges. "I believe that the HPC community needs more effective ways to bring large-scale machines to bear on a vast array of challenges," explains Parker. "Software that is easy to understand, reusable, robust, and reliable is vital to achieving the promise of HPC. We need software that can compute, manage, analyze, and visualize data in a much more straightforward manner, and it must scale to solve problems both large and small."

cibcSCI is pleased to announce the launch of our new NCRR Center for Integrative Biomedical Computing (CIBC), a five year extension of our previous NCRR center but with a new broader scope. With the new center, we will be conducting exciting research and development that builds upon the successes of previous investments, enhancing our existing strengths, and responding to a set of compelling new biomedical problems. We will continue to develop integrated problem solving environments that make advanced computational tools available to biomedical scientists. We will also continue to pursue advanced research in technical and biophysical approaches to bioelectric field problems in cardiology and neurology. Since the founding of our original NCRR Center, software research has evolved, and so too has our vision of how we can best design software to have the most impact on biomedical research. Integration is still at the core of this vision, though in order to more effectively serve researchers using other systems, we are moving away from our previous strategy of absorbing and incorporating other software into our system to what we call "bridging", in which we provide researchers with the flexibility to link to whatever software systems will meet their needs.