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.


ISBI BestPaper2013 newsCongratulations to Nikhil Singh, Jacob Hinkle, Sarang Joshi and Tom Fletcher whose paper was awarded "Best Student Paper" at the ISBI 2013 Conference.

N.P. Singh, J. Hinkle, S. Joshi, P.T. Fletcher. A Vector Momenta Formulation of Diffeomorphisms for Improved Geodesic Regression and Atlas Construction,” In IEEE Proceedings of ISBI 2013, Note: Received Best Student Paper Award, 2013.

crj-CRA newsSCI Institute Director Chris Johnson has been elected a new member of the Computing Research Association (CRA) Board of Directors. Johnson's three-year term on the board will begin July 1, 2013. The CRA “is an association of more than 200 North American academic departments of computer science, computer engineering, and related fields; laboratories and centers in industry, government, and academia engaging in basic computing research; and affiliated professional societies” (Source: CRA's mission is to strengthen research and advanced education in the computing fields, expand opportunities for women and minorities, and improve public and policymaker understanding of the importance of computing and computing research in our society. The CRA Board of Directors is made up of distinguished computing researchers in academia and industry and members are elected by their peers.

See: "2013 CRA Board Election Results"
fluorender newsWe are happy to announce the 2.12 release of FluoRender. For details, check the release notes and download FluoRender at

Release Notes

FluoRender 2.12

fresh-tracksWelcome to the first Fresh Tracks Newsletter, highlighting news from the SCI Institute. 2012 was another exciting year, culminating in our second successful SCIx Open House. Hundreds of people took advantage of the event to learn more about SCI Institute research and hear SCIx keynote speaker Alan Kay, a Turing Award recipient give an enlightening and entertaining presentation. SCI Institute faculty garnered a number of prestigious research awards in 2012. Jeff Weiss received the Van Mow Medal, Miriah Meyer was named a Microsoft Faculty Fellow and a TED Fellow, Chuck Hansen was elected as an IEEE Fellow, and Valerio Pascucci was inducted as a DOE Fellow. Tolga Tasdizen received an NSF CAREER Award and the College of Engineering Distinguished Teaching Award. I was honored to receive the 2012 IEEE IPDPS Charles Babbage Award.

Dr. Guido GerigAJPBestPaper news co-authored a paper that made the list of the American Journal of Psychiatry's "Best of 2012" for their paper “Differences in White Matter Fiber Tract Development Present from 6 to 24 Months in Infants with Autism”

In the AJP's 2012 Year in Review, the editors discuss the significance of this paper:

dongbinDongbin Xiu has joined the University of Utah's Scientific Computing and Imaging (SCI) Institute as a Professor of Mathematics. The SCI Institute focuses on solving important problems in biomedicine, science, and engineering using computation and is an international research leader in the areas of scientific computing, visualization, and image analysis.


April 3-7, 2013 Salt Lake City, Utah, USA

Chair:  Jeffrey Weiss, University of Utah

Co-Chair:  Gerard Ateshian, Columbia University

Weiss ASME-award newsCongratulations to Dr. Jeff Weiss who has been selected to receive the 2013 Van Mow Medal from the American Society of Mechanical Engineers.

This highly competitive award is ASME's highest honor for a mid-career bioengineer. Jeff was chosen "... for seminal contributions to research in bimoechanics related to fundamental structure-function relationships in musculoskeletal soft tissues, subject-specific modeling of joint mechanics, image-based biomechanics, the mechanics of angiogenesis, and the development and distribution of the FEBio software suite."
Cleaver newsThe CIBC development team is pleased to announce the release of Cleaver v1.5. Cleaver is a C++ software library that generates conforming tetrahedral meshes of multimaterial volumetric data, with guarantees on dihedral angles. Cleaver is an implementation of the "Lattice Cleaving" algorithm, developed at the SCI Institute and published in the Proceedings of the 21st International Meshing Roundtable.

For more information and downloads visit the Cleaver Software page.
scix12 newsThe Scientific Computing and Imaging (SCI) Institute hosted the second annual SCIx Open House on Tuesday, November 13th.  At SCIx, the SCI Institute put its cutting-edge work on display for the public accompanied by a keynote presentation from Alan Kay. Alan Kay is a pioneer in object oriented programming and personal computing who conceived laptops years before their realization and received the 2003 Turing Award. This year’s open house presented more stunning and innovative research.

Miriah TEDFellowCongratulations to Miriah Meyer who has been selected as a 2013 TED Fellow. This honor was granted to just 20 applicants from over 1200 applications. 

TED2013's tagline is: "The Young. The Wise. The Undiscovered." And this year's class of TED Fellows will be representing all three. The TED Fellows program brings together young innovators from around the globe, all with insightful, bold ideas that have the potential to influence our world. In addition to attending TED2013, the Fellows will go to a preconference boot camp full of advice for spreading their ideas far and wide, and get mentoring from the larger TED community.
See: TED Blog - "The Proud, the Few: the 2013 TED Fellows"