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Scientific Computing and Imaging Institute

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Coordinates: 40°46′3.72″N 111°50′42.00″W / 40.7677000°N 111.8450000°W / 40.7677000; -111.8450000
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Scientific Computing and Imaging Institute
Established1994
Research typeComputer science and translational research
Field of research
Scientific visualization, High performance computing, Image analysis
Director Chris Johnson
LocationSalt Lake City, Utah
AffiliationsUniversity of Utah School of Computing
University of Utah School of Medicine
University of Utah College of Engineering
Operating agency
University of Utah
Websitewww.sci.utah.edu

The Scientific Computing and Imaging (SCI) Institute is one of eight permanent research institutes at the University of Utah. Faculty are associated primarily with the School of Computing, Department of Bioengineering, Department of Mathematics, and Department of Electrical and Computer Engineering. Research focuses include the development of new scientific computing techniques, tools, and systems with applications to various fields, including high performance computing, scientific visualization, image analysis, computational biology, data science, and graphics.[1]

History

The Scientific Computing and Imaging Institute began as a research group started in 1992 by Dr. Chris Johnson and Dr. Rob MacLeod. In 1994 this group became the Center for Scientific Computing and Imaging, and in 2000 the name was changed to the Scientific Computing and Imaging (SCI) Institute. In 2007, the SCI Institute was awarded funding from USTAR to recruit more faculty in medical imaging technology. In 2008, the SCI Institute 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). In 2011, USTAR funding allowed faculty recruitment for genomic signal processing and information visualization.

Research

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. Given the proximity and availability of research conducted at the University of Utah School of Medicine, an important application focus is medicine. SCI Institute researchers also apply computational techniques to particular scientific and engineering sub-specialties, such as fluid dynamics, biomechanics, electrophysiology, bioelectric fields, uncertainty visualization, parallel computing, inverse problems, and neuroimaging.

The SCI Institute is known for its 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.

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 software. The latest releases and source code lives on Github. 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 image 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 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 for representing, processing, and visualizing scientific raster data.

Notable researchers

  1. ^ "Scientific Computing and Imaging Institute – Home". Retrieved 2013-04-16.

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

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