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

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.

mike-martinMike Kirby joins us from Brown University.The focus of his research focus deals with large- scale scientific computing and visualization, with an emphasis on the scientific cycle of mathematical modeling, computation, visualization, evaluation, and understanding. His primary research interests are: Computational Science and Engineering, Concurrent Programming, Scientific Visualization, Interdisciplinary Collaboration across Computer Science, Engineering, Applied Math, Computational Steering, and High Performance Computing.

Martin Berzins joins us from the University of Leeds where he is also Professor of Scientific Computing, Co-director of the Computational PDEs Unit, and head of the Scientific Computing and Visualization research group. His primary interests are in the fields of Adaptive Numerical Methods and software, Unstructured Tetrahedral Meshes, Reacting Flows, Time Dependent PDEs, Parallel Algorithms, and Computational Fluid and Solid Mechanics Applications.
scirun-1-24Thanks to everyone for their feedback on the 1.24.0-beta pre-release. Based on your suggestions, we fixed important bugs over the past few weeks, and we added many great new features as well.

This version of SCIRun/BioPSE contains a new PowerApp called "BioImage" for the processing and visualization of medical image volumes. With BioImage users can directly load a variety of native data formats (e.g. DICOM, Analyze, VFF, NRRD, PICT) and can apply processing algorithms to specify and enhance regions of interest within the volume (e.g. cropping, resampling, histogram equalization, median filtering, contrast / brightness). The BioImage visual interface allows users to interact with their data both in 2D "slice views" (powered by the new ViewSlices module), as well as in a full 3D "volume rendering view" (powered by our new high-performance volume rendering modules). Users can seamlessly move between the 2D and 3D views to precisely control how different features of their data are displayed, and to gain both quantitative and qualitative insights.

The SCI Institute is proud to announce the availability of SCIRun on the Silicon Graphics PrismTM visualization system. The combination of large memory, parallel CPUs and advanced graphics capabilities on the Silicon Graphics Prism provide an ideal platform for the SCIRun problem solving environment. The modular nature of the Silicon Graphics Prism allows scaling to meet the computational needs of the most demanding SCIRun users.

Using SCIRun's advanced volume rendering PowerApp 'BioImage' we are able to fully exploit the powerful graphics capabilities of the Prism system. The combination with BioImage, the Prism's graphics capabilities and a 64-bit architecture allow for interactive visualization of very large datasets.