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.


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.
FreshTracks-9-13 newsWelcome to the Fresh Tracks Newsletter, highlighting news from the SCI Institute. Since our first newsletter six months ago, SCI Institute faculty, staff, and students have continued to perform exciting research, lead international conferences, perform important professional service, and educate students at the graduate, undergraduate, and even high school levels.

udcc-openhouse newsWednesday, September 11th
11 am to 2 pm
University of Utah
Warnock Engineering Building, Catmull Gallary
72 So. Central Campus Dr.

The first UDCC open house will bring together our consortium partners and engineering students to a single venue. Partners interested in sponsoring student internships through the new Data Center Engineering Certificate will be present for questions, and students will have the opportunity to hear from and engage with some of our nation's leading experts in the field. You can visit our website or email us for more information.

sibgrapi2013-bestpaper newsCongratulations to Wathsala Widanagamaachchi, Paul Rosen, and Valerio Pascucci whose paper:

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W. Widanagamaachchi, P. Rosen, V. Pascucci. "A Flexible Framework for Fusing Image Collections into Panoramas," In Proceedings of the 2013 SIBGRAPI Conference on Graphics, Patterns, and Images, Note: Awarded Best Paper., pp. (to appear). 2013.

won "Best Paper" at the 2013 SIBGRAPI Conference on Graphics, Patterns, and Images. Their paper presents a new approach for the construction of panoramas called "Ray Graphs". This framework allows users to create arbitrarily shaped panoramas. In addition, this framework also allows modification of panoramas to remove undesirable objects.
NNSA-COEs newsPress Release from the National Nuclear Security Administration Website, June 27, 2013.

WASHINGTON, D.C. – The National Nuclear Security Administration (NNSA) today announced the selection of its six new centers of excellence whose primary focus will be on the emerging field of predictive science.

Six universities were selected either as a Multidisciplinary Simulation Center (MSC) or as a Single-Discipline Center (SDC). The MSCs will receive $3.2 million and the SDCs will receive $1.6 million each year for five years under NNSA's Predictive Science Academic Alliance Program II (PSAAP II) agreement.

Schott TVCG2013 newsCongratulations to Harsh Bhatia, Valerio Pascucci, and Peer-Timo Bremer, et. al. whose paper:

H. Bhatia, G. Norgard, V. Pascucci, P.-T. Bremer. The Helmholtz-Hodge Decomposition - A Survey,” In IEEE Transactions on Visualization and Computer Graphics (TVCG), Vol. 19, No. 8, pp. 1386--1404, Note: Selected as Spotlight paper for August 2013 issue, 2013.

is spotlighted in the August Issue of IEEE Transactions on Visualization and Computer Graphics (TVCG). Their paper surveys the use of the Helmholtz-Hodge Decomposition in modeling flow phenomena in various fields of science and addresses the problem of the fragmented nature of research in this area. The goal of this paper is to promote further research in the field by creating a common repository of HHD techniques and assemble a large collection of example applications in a broad range of areas. See: TVCG August 2013.

HBM Hackathon2013 newsCongratulations to Kris Zygmunt, Wei Liu, and Sean McKenna for winning the second challenge of the 2013 HBM Hackathon sponsored by Allen Institute for Brain Science and Amazon Web Services. The HBM Hackathon consisted of two challenges announced prior to the meeting and a third mystery challenge announced during the meeting. These challenges were:

1. Best imaging and gene expression relationship discovered via integration of imaging data with the Allen Human Brain Atlas.

2. Best neural systems model or visualization based on large-scale integration of resting state fMRI data with other HBM Hackathon accessible datasets.

3. MNI Mash-up: Most innovative map or aggregation of information in the MNI 152 standard.

Ross-CCC newsCongratulations to SCI faculty member Ross Whitaker who has been selected to serve on the Computing Research Association's (CRA) Computing Community Consortium (CCC). The CCC is an organization whose goal is to catalyze and empower the U.S. computing research community to pursue audacious, high-impact research. Dr. Whitaker will serve a three-year term on the council.

For more information about the CCC see
See original article on Explore Utah Science website: "When Art and Science Intertwine"
Written by  Julie Kiefer

ExpUtahScience newsThe collection of images appears to be a study in shape, color, and design. Zig-zagging lines that meld into smoke-like ribbons; an explosion of colors that seemingly blasts beyond the frame; a brain washed in pastels (see Image Gallery below). What at first glance looks like art is actually much more. Each piece is a window into scientific discovery.

EGPGV-bestpaper2013 newsCongratulations to Sujin Philip, Brian Summa, Julien Tierny, Peer-Timo Bremer, and Valerio Pascucci whose paper:

S. Philip, B. Summa, J. Tierny, P.-T. Bremer, V. Pascucci. Scalable Seams for Gigapixel Panoramas,” In Proceedings of the 2013 Eurographics Symposium on Parallel Graphics and Visualization, Note: Awarded Best Paper!, pp. (to appear). 2013.

won "Best Paper" at the 2013 Eurographics Symposium on Parallel Graphics and Visualization. Their paper presents a fast and efficient method for blending seams between images in very large panoramas composed of mosaics of smaller images. While current methods may take many hours (or even days) to blend the images composing a gigapixel panorama, the new method takes just a few minutes.
crj-FiRe2013 newsDr. Johnson will be a featured speaker at the 2013 Future in Review (FiRe 2013) conference. He will be among a number of other distinguished guests including the Secretary of the Department of Homeland Security, Mdme. Janet Napolitano. The conference will be held May 21 - 24 in Laguna Beach, California. This year's conference is unified under the theme "Digitizing the Planet." For more details visit the Future in Review website.