Scientific Computing and Imaging Institute

The SCI research group was founded in 1994 by Drs. Chris Johnson and Rob MacLeod along with five graduate students. In 1996, they became the Center for Scientific Computing and Imaging and in 2000, the SCI Institute. The Scientific Computing and Imaging (SCI) Institute is now one of eight permanent research institutes at the University of Utah and home to over 200 faculty, students, and staff. The 16 tenure-track faculty are drawn primarily from the School of Computing, Department of Bioengineering, Department of Mathematics, and Department of Electrical and Computer Engineering, and virtually all faculty have adjunct appointments in other, largely medical, departments. Recent growth in the SCI Institute has come in part from the award in 2007 from the state of Utah of a USTAR (Utah Science and Technology Advanced Research) cluster in Imaging Technology. This allowed the Institute to recruit three new faculty in image analysis: Professors Guido Gerig, Tom Fletcher, Tolga Tasdizen. During this same time period, they were also able to recruit Professor Valerio Pascucci in visualization. In 2011, USTAR funding allowed two more: Orly Alter who specializes in genomic signal processing and Miriah Meyer, who's novel biological visualization tools are revolutionizing the way scientists view and understand their data. In 2012, the SCI Institute recruited Dongbin Xiu as its latest faculty member. Dongbin is one of the most recognized names and highly cited researchers in the area of uncertainty quantification, and will make a wonderful addition to the Institute.

Over the past decade, the SCI Institute has established itself as an internationally recognized leader in visualization, scientific computing, and image analysis applied to a broad range of application domains. The overarching research objective is to conduct application-driven research in the creation of new scientific computing techniques, tools, and systems. An important application focus of the Institute continues to be biomedicine, however, SCI Institute researchers also address challenging computational problems in a variety of application domains such as manufacturing, defense, and energy. SCI Institute research interests generally fall into the areas of: scientific visualization, scientific computing and numerics, image processing and analysis, and scientific software environments. SCI Institute researchers also apply many of the above computational techniques within their own particular scientific and engineering sub-specialties, such as fluid dynamics, biomechanics, electrophysiology, bioelectric fields, parallel computing, inverse problems, and neuroimaging.

A particular hallmark of SCI Institute research is the development of innovative and robust software packages, including the SCIRun scientific problem solving environment, Seg3D, ImageVis3D, VisTrails, ViSUS, and map3d. All these packages are broadly available to the scientific community under open source licensing and supported by web pages, documentation, and users groups.

The SCI Institute either directs or is associated with several national research centers: the NIH Center for Integrative Biomedical Computing (CIBC), the DoE Scalable Data Management, Analysis, and Visualization (SDAV), the NIH National Alliance for Medical Image Computing (NA-MIC), the DoE Scientific Data Management Center, the NIH Center for Computational Biology, and the DoE Center for the Simulation of Accidental Fires and Explosions (C-SAFE). In July, 2008, SCI was chosen as one of three NVIDIA Centers of Excellence in the U.S. (University of Illinois and Harvard University are the other two NVIDIA Centers).

The academic programs available for students are outstanding. The School of Computing has collaborated with faculty in the SCI Institute to create a graduate degree in Computing, which offers tracks in Scientific Computing and Graphics (Image Analysis is planned). The physical infrastructure is also outstanding with many large-scale computing facilities at the disposal of students and trainees, perhaps most exciting is the new NVIDIA computing cluster, which, along with a new graduate course in Parallel Programming for GPUs, provides opportunities for developing unique expertise in large-scale streaming architectures. SCI faculty also provide leadership in developing educational and research tracks in biomedical engineering through the Bioengineering Department. There are undergraduate and graduate tracks in computing and imaging, in part created and directed by SCI faculty. There is also a graduate track in cardiac electrophysiology and biophysics, directed by SCI faculty and supported through collaboration between SCI and the Cardiovascular Research and Training Institute (CVRTI).

Perhaps most encouraging is the general atmosphere provided by the SCI Institute and its more than 200 members, all dedicated to some aspect of scientific computing. There is extensive expertise within the SCI Institute that covers all the topics required for simulation, modeling, and visualization including high performance computing, efficient numerical algorithms, large data management and storage, database management, and scientific visualization of all forms of scalar, vector, tensor, and volume data.

Associated research centers

The SCI Institute houses the NIH/NCRR Center for Integrative Biomedical Computing (CIBC) and is associated with several other national research centers:

Open source software releases

A CT scan of a human torso rendered with ImageVis3D

Besides research in the areas mentioned above, a particular focus of SCI has been to develop innovative and robust software packages, and release them as open source. Examples:

SCIRun, a Problem Solving Environment (PSE), for modeling, simulation and visualization of scientific problems.
BioMesh3D, a tetrahedral mesh generator, that is capable of generating multi-material quality meshes out of segmented biomedical image data.
Seg3D, an interactive segmentation tool.
ImageVis3D, a lightweight, feature-rich volume rendering application.
Visus, Visualization Streams for Ultimate Scalability.
ShapeWorks, a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization.
map3d, a scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models.
Uintah, a set of software components and libraries that facilitate the solution of partial differential equations on structured adaptive mesh refinement grids using hundreds to thousands of processors.
FiberViewer, a comprehensive, integrated, open-source environment for medical image visualization and analysis.
AtlasWerks, an open-source (BSD license) software package for medical image atlas generation.
NCR Toolset, a collection of software tools for the reconstruction and visualization of neural circuitry from electron microscopy data.
FluoRender, an interactive rendering tool for confocal microscopy data visualization.
ElVis, a visualization system created for the accurate and interactive visualization of scalar fields produced by high-order spectral/hp finite element simulations.
VisTrails, a scientific workflow management system.
Afront, a tool for meshing and remeshing surfaces.
Cleaver, A MultiMaterial Tetrahedral Meshing API and Application.
EpiCanvas, Infectious Disease Weather Map.
FEBio, is a nonlinear finite element solver that is specifically designed for biomechanical applications.
PreView, a Finite Element (FE) pre-processor that has been designed specifically to set up FE problems for FEBio
PostView, a Finite Element (FE) post-processor that is designed to post-process the results from FEBio.
STCR, a matlab-based program to reconstruct undersampled DCE radial data, with Compressed Sensing methods.
ExoshapeAccel, a C/C++ application for estimating continuous evolution from a discrete collection of shapes, designed to produce realistic anatomical trajectories.
VISPACK, a C++ library that includes matrix, image, and volume objects.
Teem, a collection of libraries written by Gordon Kindlmann (in C) in support of his research.

External links

40°46′3.72″N 111°50′42.00″W / 40.7677000°N 111.8450000°W / 40.7677000; -111.8450000