Scientific Computing and Imaging Institute: Difference between revisions

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{{Short description|Research institute at the University of Utah}}

The SCI research group was founded in 1994 by Drs. '''[http://www.sci.utah.edu/people/crj.html Chris Johnson]''' and '''[http://www.sci.utah.edu/people/macleod.html Rob MacLeod]''' along with five graduate students. In 1996, we became the Center for Scientific Computing and Imaging and in 2000, the SCI Institute. '''[http://www.sci.utah.edu The Scientific Computing and Imaging (SCI) Institute]''' is now one of eight permanent research institutes at the [http://www.utah.edu/ University of Utah] and home to nearly 200 faculty, students, and staff. The 15 tenure-track faculty are drawn primarily from the School of Computing, Department of Bioengineering, 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 ([http://business.utah.gov/programs/science-advisor/wired/WIRED-Partners/ustarinitiative/ Utah Science and Technology Advanced Research]) cluster in Imaging Technology. This allowed the Institute to recruit fournew faculty in image analysis: Professors [http://www.sci.utah.edu/people/gerig.html Guido Gerig], [http://www.sci.utah.edu/people/fletcher.html Tom Fletcher], [http://www.sci.utah.edu/people/tolga.html Tolga Tasdizen], and [http://www.sci.utah.edu/people/orly.html Orly Alter]. During this same time period, we were also able to recruit Professor [http://www.sci.utah.edu/people/pascucci.html Valerio Pascucci] in visualization and Professor Juliana Freire in scientific data management.

{{More citations needed|date=May 2021}}

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{{Infobox research institute

|name = Scientific Computing and Imaging Institute

|motto =

|image = Warnock Engineering Building, University of Utah.tif

|established = 1994

|type = [[Computer science]] and [[translational research]]

|budget =

|debt =

|research_field = [[Scientific visualization]], [[High performance computing]], [[Image analysis]]

|director = Dr. Manish Parashar

|head =

|faculty =

|staff =

|students =

|undergrad =

|postgrad =

|doctoral =

|postdoc =

|profess =

|alumni =

|city = [[Salt Lake City, Utah]]

|address =

|telephone =

|campus =

|free =

|affiliations = [[University of Utah School of Computing]]<br/>[[University of Utah School of Medicine]]<br/>[[University of Utah College of Engineering]]

|operating_agency = [[University of Utah]]

|nobel_laureates =

|website = [http://www.sci.utah.edu/ www.sci.utah.edu]

|logo =

|footnotes =

}}

The '''Scientific Computing and Imaging (SCI) Institute''' is a permanent [[research institute]] at the [[University of Utah]] that focuses on the development of new [[scientific computing]] and [[scientific visualization|visualization]] techniques, tools, and systems with primary applications to [[biomedical engineering]].<ref>{{cite web|title=Scientific Computing and Imaging Institute – Home|url=http://www.sci.utah.edu/home.html|access-date=2013-04-16}}</ref><ref>{{cite book|last1=Lipson|first1=Hod|last2=Kurman|first2=Melba|title=Fabricated: The New World of 3D Printing|date=2013|publisher=Wiley|___location=Indianapolis, IN|isbn=978-1118350638|page=121}}</ref> The SCI Institute is noted worldwide in the [[visualization (graphics)|visualization]] community for contributions by faculty, alumni, and staff.<ref>{{cite book|last1=Shneiderman|first1=Ben|title=The New ABCs of Research: Achieving Breakthrough Collaborations|publisher=Oxford University Press|___location=Oxford|isbn=978-0-19-875883-9|pages=320}}</ref> Faculty are associated primarily with the [[University of Utah School of Computing|School of Computing]], Department of Bioengineering, Department of Mathematics, and Department of Electrical and Computer Engineering, with auxiliary faculty in the [[University of Utah Medical School|Medical School]] and [[University of Utah College of Architecture and Planning|School of Architecture]].

==History==

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 different areas: 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.

The Scientific Computing and Imaging Institute started in 1992 as a research group in the [[University of Utah School of Computing]] by [[Christopher R. Johnson|Chris Johnson]] and 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. The SCI Institute was recognized as an [[Nvidia|NVIDIA]] [[CUDA]] Center of Excellence in 2008.<ref>{{cite web|last1=Humber|first1=Andrew|title=NVIDIA Recognizes University Of Utah As A Cuda Center Of Excellence|url=http://www.nvidia.com/object/io_1217508281856.html|publisher=NVIDIA|access-date=8 April 2017|language=en-us|date=31 July 2008}}</ref> In 2011, [[USTAR]] funding allowed faculty recruitment for genomic [[signal processing]] and information visualization. in 2014, [[Intel]] partnered with the SCI Institute to form the Intel Parallel Computing Center for Scientific Rendering to research and develop large scale and in situ visualization techniques for Intel hardware.<ref>{{cite web|title=Intel® Parallel Computing Center at SCI Institute, University of Utah {{!}} Intel® Software|url=https://software.intel.com/en-us/articles/intel-parallel-computing-center-at-sci-institute-university-of-utah|website=Intel Developer Zone|access-date=8 April 2017|language=en|date=16 September 2014}}</ref>

==Research==

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

The overarching research objective of the Scientific Computing and Imaging Institute is to conduct [[applied science|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]], a main application focus is [[medicine]]. SCI Institute researchers also apply computational techniques to scientific and engineering sub-specialties, such as [[fluid dynamics]], [[biomechanics]], [[electrophysiology]], bioelectric fields, [[scientific visualization]], [[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, 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 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 Bioengineeeing 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 [http://www.cvrti.utah.edu/ Cardiovascular Research and Training Institute (CVRTI)].

== Associated research centers ==

The SCI Institute houses the NIH/NCRR Center for Integrative Biomedical Computing (CIBC)<ref>{{cite web|url=http://www.sci.utah.edu/cibc/|title=CIBC Homepage}}</ref> and is associated with several other national research centers:

* [http://sdav.sci.utah.edu/ DoE Scalable Data Management, Analysis, and Visualization (SDAV)]

* [http://mrl.sci.utah.edu/ Musculoskeletal Research Laboratories (MRL)]

* [http://csafe.sci.utah.edu/ DoE Center for the Simulation of Accidental Fires and Explosions (C-SAFE)]

* [http://alterlab.org/ Orly Alter Genomic Signal Processing Lab (alterlab.org)]

* [http://cedmav.sci.utah.edu/ Center for Extreme Data Management, Analysis, and Visualization (CEDMAV)]

* [http://ucnia.org/ Utah Center for Neuroimage Analysis (UCNIA)]

* [http://sage.sci.utah.edu/ Scalable Analysis; Group Expertise (SAGE)]

* [http://netl.sci.utah.edu/ DoE Unconventional and Renewable Energy Research Utilizing Advanced Computer Simulations (DOENETL)]

* [http://www.openwfm.org/wiki/Main_Page Open Wildland Fire Modeling e-Community]

* [http://www.sci.utah.edu/nvidia-coe.html NVIDIA CUDA Center of Excellence]

* [http://cde3m.sci.utah.edu/ Alliance for Computationally-guided Design of Energy Efficient Electronic Materials (CDE3M)]

* DoE Scientific Data Management Center

* DoE Center for Technology for Advanced Scientific Component Software (TASCS)

* [http://www.na-mic.org/ NIH National Alliance for Medical Image Computing (NA-MIC)]

* NIH Center for Computational Biology.

== Open source software releases ==

[[Image:Iv3d-torso.png|250px|thumb| A [[Computed tomography|CT]] scan of a human torso rendered with ImageVis3D]]

[[File:A-Volumetric-Method-for-Quantifying-Atherosclerosis-in-Mice-by-Using-MicroCT-Comparison-to-En-Face-pone.0018800.s006.ogv|thumb|[[Voxel|Volumetric data]] of an [[aorta]] labeled with regions of interest using [[Seg3D]] and then interactively rendered in [[SCIRun]].]]

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:

The SCI Institute releases [[Open-source software|open source]] [[package (package management system)|software packages]] for many of the projects developed by researchers for use by the [[scientific visualization]] and [[medical imaging]] communities. All projects are released under the [[MIT software license]]. Notable projects released by SCI include:

* [[SCIRun]] - [[Problem Solving Environment]] (PSE), for modeling, simulation and visualization of scientific problems

* ImageVis3D - [[volume rendering]] application with multidimensional [[transfer function]] visualization support

* [[Seg3D]] - interactive [[image segmentation]] tool

* [[ViSUS]] - Visualization Streams for Ultimate Scalability

* [[ShapeWorks]] - [[statistical shape analysis]] tool that constructs compact statistical point-based models of ensembles of similar shapes that does not rely on any specific [[surface parameterisation|surface parameterization]]

* [[FluoRender]] - interactive rendering tool for [[confocal microscopy]] data visualization.

* [[VisTrails]] - [[scientific workflow system|scientific workflow management system]].

* [[Cleaver]] - multi-material [[image-based meshing|tetrahedral meshing]] API and application

* [[FEBio]] - nonlinear [[finite element solver]] specifically designed for biomechanical applications

* [[VISPACK]] - C++ library that includes matrix, image, and volume objects

* [[Teem]] - collection of libraries for representing, processing, and visualizing scientific [[raster data]]

* [[Manta Interactive Ray Tracer]] - interactive [[ray tracing (graphics)|ray tracing]] environment designed for both workstations and supercomputers

==Notable researchers and alumni==

* [http://www.sci.utah.edu/software/scirun.html SCIRun], a Problem Solving Environment (PSE), for modeling, simulation and visualization of scientific problems.

*[[David M. Beazley]] - wrote ''Python Essential Reference'', co-awarded the [[Gordon Bell Prize]] in 1993 and in 1998

* [http://www.sci.utah.edu/software/biomesh3d.html BioMesh3D], a tetrahedral mesh generator, that is capable of generating multi-material quality meshes out of segmented biomedical image data.

*[[Juliana Freire]] - developed [[VisTrails]], Fellow of the [[Association for Computing Machinery]]

* [http://www.sci.utah.edu/software/seg3d.html Seg3D], an interactive segmentation tool.

*[[Amy Ashurst Gooch]] - developed [[Gooch shading]] for [[non-photorealistic rendering|non-photo realistic rendering (NPR)]], authored first book on NPR

* [http://www.sci.utah.edu/software/imagevis3d.html ImageVis3D], a lightweight, feature-rich volume rendering application.

*[[Charles D. Hansen]] - co-editor of ''[[The Visualization Handbook]]''

* [http://www.sci.utah.edu/software/shapeworks.html 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.

*[[Gordon Kindlmann]] - developed [[tensor glyph]]s

* [http://www.sci.utah.edu/software/map3d.html map3d], a scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models.

*[[Aaron Lefohn]] - Director of Research at [[NVIDIA]]

* [http://www.sci.utah.edu/software/528-uintah.html 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.

* [[Miriah Meyer]] - [[TED Fellow]] and [[MIT Technology Review]] [[TR35]] listee, pioneer in [[interactive visualization]] for [[basic research]]

* [http://www.sci.utah.edu/software/fiberviewer.html FiberViewer], a comprehensive, integrated, open-source environment for medical image visualization and analysis.

*[[Erik Reinhard]] - Distinguished Scientist at [[Technicolor SA|Technicolor Research and Innovation]], founder and Editor-in-Chief for ''[[ACM Transactions on Applied Perception]]''

* [http://www.sci.utah.edu/software/370-atlaswerks.html AtlasWerks], an open-source (BSD license) software package for medical image atlas generation.

*[[Theresa-Marie Rhyne]] - founding director of the [[SIGGRAPH]] Cartographic Visualization Project and the [[United States Environmental Protection Agency|Environmental Protection Agency]] Scientific Visualization Center

* [http://www.sci.utah.edu/software/129-ncrtoolset.html NCR Toolset], a collection of software tools for the reconstruction and visualization of neural circuitry from electron microscopy data.

*[[Peter Shirley]] - Distinguished Scientist at [[NVIDIA]] recognized for contributions to real time [[ray tracing (graphics)|ray tracing]]

* [http://www.sci.utah.edu/software/127-fluorender.html FluoRender, an interactive rendering tool for confocal microscopy data visualization.

*[[Claudio Silva (computer scientist)|Claudio Silva]] - chair of [[IEEE Computer Society]] [[Technical Committee on Visualization and Graphics]], developed [[VisTrails]]

* [http://www.sci.utah.edu/software/546-elvis.html ElVis], a visualization system created for the accurate and interactive visualization of scalar fields produced by high-order spectral/hp finite element simulations.

*[[Peter-Pike Sloan]] - developed the [[precomputed radiance transfer]] rendering method

* [http://www.sci.utah.edu/software/41-nsf/40-vistrails VisTrails], a scientific workflow management system.

*[[Ross Whitaker]] - director of the [[University of Utah School of Computing]] and [[IEEE Fellow]]

* [http://www.sci.utah.edu/software/41-nsf/112-afront Afront], a tool for meshing and remeshing surfaces.

* [http://www.sci.utah.edu/software/cleaver.html Cleaver], A MultiMaterial Tetrahedral Meshing API and Application.

* [http://www.sci.utah.edu/software/epicanvas.html EpiCanvas], Infectious Disease Weather Map.

* [http://www.sci.utah.edu/software/40-mrl/39-febio FEBio], is a nonlinear finite element solver that is specifically designed for biomechanical applications.

* [http://www.sci.utah.edu/software/40-mrl/108-preview PreView], a Finite Element (FE) pre-processor that has been designed specifically to set up FE problems for FEBio

* [http://www.sci.utah.edu/software/40-mrl/109-postview PostView], a Finite Element (FE) post-processor that is designed to post-process the results from FEBio.

* [http://www.sci.utah.edu/bisti.html STCR], a matlab-based program to reconstruct undersampled DCE radial data, with Compressed Sensing methods.

* [http://www.sci.utah.edu/software/627-exoshapeaccel.html ExoshapeAccel], a C/C++ application for estimating continuous evolution from a discrete collection of shapes, designed to produce realistic anatomical trajectories.

* [http://www.sci.utah.edu/software/39-libraries/110-vispack VISPACK], a C++ library that includes matrix, image, and volume objects.

* [http://www.sci.utah.edu/software/39-libraries/111-teem Teem], a collection of libraries written by Gordon Kindlmann (in C) in support of his research.

== External links ==

*[https://github.com/SCIInstitute SCI Institute GitHub]

<references/>

*[http://www.sci.utah.edu/~nathang/history/SCI-History.pdf Scientific Computing and Imaging Institute: A History]

==References==

{{Reflist}}

{{University of Utah}}

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