Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Large scale visualization on the Powerwall.
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.


shapeworksThe ShapeWorks software is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results. Download ShapeWorks.
chris-siamSCI Director Dr. Chris Johnson has been selected by the Society for Industrial and Applied Mathematics (SIAM) to be honored as a SIAM Fellow for his contributions to Scientific Computing and Visualization. The SIAM Fellow is a new honor designed to recognize a member's outstanding contributions to the fields served by SIAM. Dr. Johnson is among the initial class to be selected for this honor. Initial Fellows were selected from among those SIAM members for which certain previous recognition places them clearly among those intended to be recognized by the program. For more information see: SIAM Fellows Program.
nvidiaSCI graduate student Huy Vo has been awarded an NVIDIA Fellowship for 2009-2010. Huy is one of just ten students in the country to receive this honor. The NVIDIA Fellowship Program provides funding to Ph.D. students who are conducting research on topics which are expected to lead to major advances in the graphics and digital media industry, and are investigating innovative ways of leveraging the power of graphics hardware. Huy Vo's graduate adviser is SCI faculty member Dr. Cláudio T. Silva.

For more information about the award, please see the NVIDIA press release "NVIDIA Fellowship Results for 2009"
sci-moranA SCI research team, lead by Dr. Tolga Tasdizen and Dr. Ross Whitaker, in collaboration with Dr. Robert Marc and his team at the Moran Eye Center have recently completed a 3D neurocircuitry map of every cell in the retina of a rabbit's eye. This data is a huge milestone on the way to building a complete description of the neurocircuitry that allows mammals to see. By comparing healthy samples with those undergoing disease processes, neuroscientists hope to develop a detailed understanding of how many diseases cause blindness and hopefully find ways to stop or even reverse the deterioration. The Neural Circuit Reconstruction Toolset used to construct this unprecedented map from thousands of individual electron microscope images was developed here at the SCI Institute and is currently available for download for free. The massive 20GB dataset will also eventually be made available on the web. 

vt-mayaCongratulations are in order to the VisTrails team. Their Provenance Explorer for Maya has won the Utah 2009 Innovation Award.

VisTrails Inc., a SCI spin off company, was one of just nine companies to be awarded a Utah Innovation award for 2009. This award is designed to recognize Utah companies that make important innovations in their industries. A committee of more than 70 experts from private industry, government and higher education selected the award winners. Vistrails, Inc. was recognized in the Enterprise B-2-B Software category for it's Provenance Explorer for Maya.

For more information see: SL Tribune - "Utah's innovative spirit on display in Salt Lake City"
wfmSCI, in collaboration with the National Center for Atmospheric Research (NCAR) and the University of Colorado at Denver have teamed up to tackle the challenges associated with modeling the complexities of wildfires.

The losses associated with wildfires and the wish to understand, predict, and control wildfires have driven researchers to create ever more detailed and powerful computational models. However, the necessary sophistication and realism requires scientific computing and analysis processes of a complexity that has itself become a hindrance to further progress and education. In addition, the research is done by geographically disperse interdisciplinary groups, and making their models interoperate is a challenge. This project strives to overcome this complexity and challenges to collaboration by state-of-the-art software engineering, visualization, and collaboration tools. The results will find applications in wildfire research, education, training, and management.

v100-09Congratulations go out to our Associate Director Greg Jones who was recently designated a v|100 - vSpring Top 100 Venture Entrepreneur. The v|100 designation is given to those individuals voted most likely to lead a successful business venture in Utah within the next few years. The v|100 is designed to help entrepreneurs and vSpring Capital establish and cultivate relationships among top CEO and CTO talent in the region. Members of this elite executive community are chosen through a peer-nominated and peer-selected process. Top members of the Utah business community were surveyed by a vSpring team to nominate the top 100 ventrue entrepreneurs in Utah. 2009 marks the sixth year of the v|100 Community. Greg was also selected as a v|100 member in 2008 and 2005.
scirun-4-0The NIH/NCRR Center for Integrative Biomedical Computing (CIBC) is pleased to announce the release of the 4.0 version of the SCIRun software suite. SCIRun is a problem solving environment for biomedical problems that is based on a dataflow paradigm. The new version contains many bug fixes, a new interface and many new modules. The new 4.0 version is now available as binary download for both OS X and Windows XP/Vista as well as a source download for other platforms.

To download the new SCIRun version 4.0, go to our CIBC Software portal.
For questions and further information on the 4.0 SCIRun release, please visit the CIBC webiste software page.
libraryThe SCI Institute, in partnership with the Department of Radiology has been working towards new goals in public outreach. A three-part exhibit is now on display at the Salt Lake Public Library and includes hands-on multi-media, Q and A from the University's leading radiologists, a four lecture series, and a 20 piece gallery display which will run through December. Overall, it has been a great success and has opened the public eye to a glimpse of what we are working on.

afibBy Rob MacLeod, Professor and Associate Chair of Undergraduate Studies, Department of Bioengineering

Atrial fibrillation is the most common – and perhaps most insidious – form of heart rhythm disturbance, affecting 2.5 million Americans. While usually not life-threatening in its initial stages, the condition can eventually lead to a stroke or heart attack. Finding better ways to treat atrial fibrillation is the focus of a group of bioengineers in the College of Engineering who have teamed up with imaging physicists and physicians in the School of Medicine.