Scientific Computing and Imaging Institute: Difference between revisions

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

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[[Image:Warnock Engineering Building, University of Utah.tif|thumb|Warnock Engineering Building, University of Utah]]

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The '''Scientific Computing and Imaging (SCI) Institute''' is one of eight permanent research institutes at the [[University of Utah]] and home to over 200 faculty, students, and staff. 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. 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]].<ref>{{cite web|title=Scientific Computing and Imaging Institute – Home|url=http://www.sci.utah.edu/home.html|accessdate=2013-04-16}}</ref>

{{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==

The Scientific Computing and Imaging Institute beganstarted in 1992 as a research group started in 1992the by[[University Dr.of Utah School of Computing]] by [[Christopher R. Johnson|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, theThe SCI Institute was chosenrecognized as one of threean [[Nvidia|NVIDIA]] Centers[[CUDA]] Center of Excellence in the U.S2008.<ref>{{cite ([[Universityweb|last1=Humber|first1=Andrew|title=NVIDIA ofRecognizes Illinois]]University andOf [[HarvardUtah University]]As areA theCuda otherCenter twoOf Excellence|url=http://www.nvidia.com/object/io_1217508281856.html|publisher=NVIDIA|access-date=8 Centers).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>

==Academics==

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 [http://www.cvrti.utah.edu/ Cardiovascular Research and Training Institute (CVRTI)].

==Research==

OverThe theoverarching pastresearch decade,objective of the SCIScientific Institute has established itself as an internationally recognized leader in visualization, scientific computing,Computing and imageImaging analysis applied to a broad range of application domains. The overarching research objectiveInstitute 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]], ana importantmain 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[[scientific visualization]], [[parallel computing]], [[inverse problems]], and [[neuroimaging]].

The SCI Institute is known for its development of innovative and robust software packages, including the [http://www.scirun.org SCIRun scientific problem solving environment], [http://www.seg3d.org Seg3D], [[ImageVis3D]], [[VisTrails]], [https://visus.us/ ViSUS], and [http://www.sci.utah.edu/software/map3d.html map3d]. All these packages are broadly available to the scientific community under [[open-source software|open source licensing]] and supported by web pages, documentation, and users groups.

== Associated research centers ==

The SCI Institute houses the '''[http://www.sci.utah.edu/cibc NIH/NCRR Center for Integrative Biomedical Computing (CIBC)]''' 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://netl.sci.utah.edu/ DoE Unconventional and Renewable Energy Research Utilizing Advanced Computer Simulations (DOE/NETL)]

* [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)]

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

* [http://iamcs.tamu.edu/ Institute for Applied Mathematics and Computational Science (IAMCS/KAUST)]

* CDC Decision-Support for Infectious Disease Epidemiology

== 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|open-source software]]. The latest releases and source code lives on [https://github.com/SCIInstitute Github]. 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:

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

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

* [http://www.biomesh3d.org BioMesh3D], a tetrahedral [[mesh generation|mesh generator]], that is capable of generating multi-material quality meshes out of segmented biomedical image data.

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

* [http://www.seg3d.org Seg3D], an interactive [[image segmentation]] tool.

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

* [[ImageVis3D]], a lightweight, feature-rich [[volume rendering]] application.

* [https://visus.us/ Visus[ViSUS],] - Visualization Streams for Ultimate Scalability.

* [http://www.sci.utah.edu/software/shapeworks.html [ShapeWorks],] a- new[[statistical methodshape foranalysis]] tool that constructingconstructs 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.

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

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

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

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

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

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

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

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

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

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

* [http://www.fluorender.org FluoRender], an interactive rendering tool for [[confocal microscopy]] data visualization.

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

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

* [[VisTrails]], a [[scientific workflow system|scientific workflow management system]].

==Notable researchers and alumni==

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

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

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

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

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

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

* [http://www.febio.org FEBio], is a nonlinear finite element solver that is specifically designed for biomechanical applications.

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

* [http://www.febio.org/software/preview PreView], a Finite Element (FE) [[preprocessor|pre-processor]] that has been designed specifically to set up FE problems for FEBio

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

* [http://www.febio.org/software/postview PostView], a Finite Element (FE) [[finite element model data post-processing|post-processor]] that is designed to post-process the results from FEBio.

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

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

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

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

*[[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/vispack.html VISPACK], a C++ library that includes matrix, image, and volume objects.

*[[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/teem.html Teem], a collection of libraries for representing, processing, and visualizing scientific [[raster data]].

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

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

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

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

== 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}}

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