SCI to Collaborate on Three New SciDAC Centers
The 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.
SCI Grad Student Helps Solve Open Problem in Computational Geometry
SCI 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.
Dr. Sarang Joshi joins SCI Institute
Dr. 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.
Steve Corbató Named Associate Director of the Scientific Computing and Imaging Institute
Steve 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.
Embryos Exposed in 3-D
New Method Can Identify What Genes Do, Test Drugs' Safety
May 4, 2006 -- Utah and Texas researchers combined miniature medical CT scans with high-tech computer methods to produce detailed three-dimensional images of mouse embryos – an efficient new method to test the safety of medicines and learn how mutant genes cause birth defects or cancer."Our method provides a fast, high-quality and inexpensive way to visually explore the 3-D internal structure of mouse embryos so scientists can more easily and quickly see the effects of a genetic defect or chemical damage,” says Chris Johnson, a distinguished professor of computer science at the University of Utah.
A study reporting development of the new method – known as “microCT-based virtual histology” – was published recently in PLoS Genetics, an online journal of the Public Library of Science.
The study was led by Charles Keller, a pediatric cancer specialist who formerly worked as a postdoctoral fellow in the laboratory of University of Utah geneticist Mario Capecchi. Keller now is an assistant professor at the Children's Cancer Research Institute at the University of Texas Health Science Center in San Antonio.
VisTrails: A New Paradigm for Dataflow Management
 Figure 1: The VisTrails Visualization Spreadsheet. Surface salinity variation at the mouth of the Columbia River over the period of a day. The green regions represent the fresh-water discharge of the river into the ocean. A single vistrail specification is used to construct this ensemble. Each cell corresponds to a single visualization pipeline specification executed with a different timestamp value. |
The Mechanics of Angiogenesis
 Growth of new blood vessels from existing ones. |
The Center for Interactive Ray-Tracing and Photo Realistic Visualization
Almost every modern computer comes with a graphics processing unit (GPU) that implements an object-based graphics algorithm for fast 3-D graphics. The object-based algorithm in these chips was developed at the University of Utah in the 1970s. While these chips are extremely effective for video games and the visualization of moderately sized models, they cannot interactively display many of the large models that arise in computer-aided design, film animation, and scientific visualization. Researchers at the University of Utah have demonstrated that image-based ray tracing algorithms are more suited for such large-scale applications. A substantial code base has been developed in the form of two ray tracing programs. The new Center aims to improve and integrate these programs to make them appropriate for commercial use.
Top Scientific Visualization Research Problems
Scientific visualization as currently understood and practiced is still a relatively new discipline. As a result, we visualization researchers are not necessarily accustomed to undertaking the sorts of self-examinations that other scientists routinely undergo in relation to their work. Yet if we are to create a disciplinary culture focused on matters of real scientific importance and committed to real progress, it is essential that we ask ourselves hard questions on an ongoing basis. What are the most important research issues facing us? What underlying assumptions need to be challenged and perhaps abandoned? What practices need to be reviewed? In this article, I attempt to start a discussion of these issues by proposing a list of top research problems and issues in scientific visualization. [PDF version]
CT Segmentation and 3-D Reconstruction with Morphometric Analysis for Evaluation of Occipital-Cervical Instability in Children
Down syndrome is a common chromosomal disorder that affects 0.15 percent of the total population. Individuals with Down syndrome are prone to spinal instability due to congenital abnormalities in the occipital-cervical (O-C1) joint near the base of the skull. To determine the possible abnormality causing this instability, an image-processing pipeline was created by combining several available software packages and custom made software. Patients with Down syndrome and spinal instability at the O-C1 joint were age-matched with controls. The subject data was assessed and a congenital abnormality was defined in the superior articular facets of C1 in the Down syndrome patients. The software developed helped to visualize the abnormality and could be used in a clinical setting to help aide in the diagnosis and screening for spinal instability in Down syndrome patients.