Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.


Hackdance newsSCI Graduate student Michael Liu was a key member on the team that took the Social Impact award at "Hackdance", the first ever celebrity-driven hackathon at the Sundance Film Festival. The team, working with celebrity member Sarah Austin (Start­Ups: Silicon Valley on Bravo), developed a prototype browser extension that monitors cyber bullying. Once installed, the extension uses a parts of speech tagger to look for harrassing comments and sentences in any conversations or content. If language is detected in their child's feed that is related to cyberbulling they are sent an alert message via email immediately. The team, which included fellow members Faris Chebib, Joe Reis, Sam Hart and Eric Smith, was awarded a $5,000 investment from the University of Utah’s Sorensen Global Impact Investment Center plus $10,000 worth of business incubation and a trip to meet Jim Sorensen. Congratulations Michael!

For more information see: Silicon Bayou News: First Celebrity-Driven, Social Impact Hackathon Makes Splash at Sundance
blood-vessel-growth Jan2014 newsJan. 22, 2014 – University of Utah bioengineers showed that tiny blood vessels grow better in the laboratory if the tissue surrounding them is less dense. Then the researchers created a computer simulation to predict such growth accurately – an early step toward treatments to provide blood supply to tissues damaged by diabetes and heart attacks and to skin grafts and implanted ligaments and tendons.

ChrisRoss IEEEFellows newsCongratulations to Professors Chris Johnson and Ross Whitaker who have been elected IEEE Fellows for the class of 2014. Dr. Johnson was elected in recognition of his leadership in scientific computing and scientific visualization. Dr. Whitaker is recognized for contributions to image and geometry processing, visualization, and medical image analysis. This honorary designation is limited to no more than one-tenth of one percent of the total voting IEEE Institute membership each year.
itkSNAP3 newsThe itk-SNAP project, a collaboration between UPenn's Paul Yushkevich and SCI's Guido Gerig, has released a major new version 3.0. SNAP is a software application used to segment structures in 3D medical images. It provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. In addition to these core functions, SNAP provides a number of supporting utilities. Version 3.0 is the first major release of itk-SNAP that is funded by the NIH grant R01 EB014346, "Continued development and maintenance of the itk-SNAP 3D image segmentation software." This version includes an almost complete rewrite of the software, along with new features focused on multi-modality image support.

For more information and downloads please visit the itk-SNAP project website.
crj-fernbach-award2013b newsCongratulations to Professor Chris Johnson who was awarded the IEEE Computer Society 2013 Sidney Fernbach Award at Supercomputing 2013. This award recognizes Professor Johnson "For outstanding contributions and pioneering work introducing computing, simulation, and visualization into many areas of biomedicine."

The Sidney Fernbach Award is one of the IEEE Computer Society's highest awards, and recognizes outstanding contributions in the application of high performance computers using innovative approaches. The award also includes a $2,000 honorarium.

scirun-4-7The SCIRun development team is pleased to announce the release of SCIRun 4.7 with meshing tools. SCIRun 4.7 is available as a binary download for Windows and OS X, and as a source download for Linux.

Download Now
Click on the Download SCIRun link, and then select the distribution for your platform.

utahdata-certificate newsPress Release from The Utah Daily Chronicle
By Nathan Turner on October 7, 2013.
Contact Nathan Turner at This email address is being protected from spambots. You need JavaScript enabled to view it..

The October session of the Academic Senate approved a proposed cross-disciplinary certificate to the College of Engineering and Scientific Computing and Imaging Institute on Monday evening.

visus-david newsThe first gigapixel, multi-view rendering of The Digital Michelangelo Project's David can now be downloaded and viewed on your iPhone, iPad, or iPod touch. The ViSUS Gigapixel David app allows you to explore the digital laser-scan of the statue David in extreme detail. With a simple pinch or spread of the fingers, users may zoom in and out to explore such details as the drill marks and scratches left by the artist Michelangelo. The David model consists of 933 million triangles from a laser-scan of the original statue created by Professor Marc Levoy and members of The Digital Michelangelo Project at Stanford University. The original data is made of 8 million polygons, each about 2.0 mm in size, smaller than the thickness of 2 dimes.

Miriah-PopTech2013 newsCongratulations to Miriah Meyer who has been chosen as a 2013 PopTech Science Fellow! PopTech's Fellows programs aim to accelerate the impact of emerging innovators and scientists, who are working to solve some of the world's most pressing challenges. Miriah is being recognized for her work in the development of visualization systems that support exploratory, complex data analysis tasks and help scientists make sense of complex data. For more information see:

PopTech Science Fellows Class of 2013
MBIA-bestpaper2013 newsCongratulations to Bo Wang, Marcel Prastawa, Avishek Saha, Suyash Awate, Andrei Irimia, Micah Chambers, Paul Vespa, John Van Horn, Valerio Pascucci, and Guido Gerig whose paper:

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B. Wang, M. Prastawa, A. Saha, S.P. Awate, A. Irimia, M.C. Chambers, P.M. Vespa, J.D. Van Horn, V. Pascucci, G. Gerig. “Modeling 4D changes in pathological anatomy using domain adaptation: analysis of TBI imaging using a tumor database,” In Proceedings of the 2013 MICCAI-MBIA Workshop, Lecture Notes in Computer Science (LNCS), Vol. 8159, Note: Awarded Best Paper!, pp. 31--39. 2013.
DOI: 10.1007/978-3-319-02126-3_4

maljovec bp-runnerup-PSA2013 newsCongratulations to Dan Maljovec, et. at, whose paper was chosen first runner-up for Best Student Paper at the 2013 International Topical Meeting on Probabilistic Safety Assessment and Analysis (PSA). See:

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D. Maljovec, B. Wang, D. Mandelli, P.-T. Bremer, V. Pascucci. “Adaptive Sampling Algorithms for Probabilistic Risk Assessment of Nuclear Simulations,” In Proceedings of the 2013 International Topical Meeting on Probabilistic Safety Assessment and Analysis (PSA 2013), Note: First runner-up for Best Student Paper Award, pp. (accepted). 2013.