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.

News

Bei 683x1024University of Utah School of Computing assistant professor Bei Wang was awarded more than $832,000 from the U.S. Department of Energy’s Early Career Research Program, one of only 75 scientists in the nation and the only faculty member from the U to earn the award this year.

Wang’s project, titled “Topology-Preserving Data Sketching for Scientific Visualization,” will conduct a study of topology-preserving data sketching techniques to improve visual exploration and understanding of large scientific data.

As scientific simulations generate a large amount of data while the simulation is running, it has become challenging to keep track of interesting phenomena and apply appropriate actions such as storage, analysis, and visualization.

Data sketching uses ideas from statistics, geometry, and linear algebra to generate an approximation of each data instance for fast and efficient processing. At the same time, visualization plays an important role in a data processing pipeline. Topology-based methods in visualization provide powerful tools to summarize and present large and complex data in a simple and easy-to-understand way.

Wang’s project combines ideas from data sketching with topological techniques in visualization. The multidisciplinary project will be universally applicable in many scientific areas, including but not limited to computational fluid dynamics and materials science.

Wang, who is also a faculty member in the U’s Scientific Computing and Imaging Institute, is focused on the analysis and visualization of large and complex data. Her research interests include topological data analysis, data visualization, computational topology, computational geometry, machine learning, and data mining. She received a bachelor’s in computer science and mathematics from the University of Bridgeport and a doctorate in computer science from Duke University.

The Early Career Research Program, now in its eleventh year, is designed to “bolster the nation’s scientific workforce by providing support to exceptional researchers during crucial early career years,” according to the DOE. Awards are given to projects related to advanced scientific computing, basic energy sciences, biological and environmental research, fusion energy sciences, high energy physics and nuclear physics.
shapeworks 5 4We are excited to announce the new release of our software, ShapeWorks 5.4. ShapeWorks is now faster and uses less memory, with a scalable graphic user interface for large cohorts and a flexible, user-friendly project file format.

To download installation packages for Windows/Mac/Linux and/or the source code, please visit https://github.com/SCIInstitute/ShapeWorks/releases/tag/v5.4.1

Proof of principle study highlights mathematical methods that are uniquely suited for personalized medicine

For the past 70 years, the best indicator of life expectancy for a patient with glioblastoma (GBM) — the most common and the most aggressive brain cancer — has simply been age at diagnosis. Now, an international team of scientists has experimentally validated a predictor that is not only more accurate but also more clinically relevant: a pattern of co-occurring changes in DNA abundance levels, or copy numbers, at hundreds of thousands of sites across the whole tumor genome.

Conferences may be a little different this year, but that hasn't stopped SCI students from showing what they're made of. This week four publications were selected as finalists in two seperate conferences.  Adam Rauff and Steven LaBelle were selected as finalists for the (virtual) student PhD paper competition at the Summer Biomechanics, Bioengineering and Biotransport Conference in June (SB3C). At this same conference Jason Manning was selected as a finalist in the undergraduate student paper competition.

zengerCongradulations to Brian Zenger on receiving a 2020-21 University Graduate Fellowship. The award includes an $18,900 scholarship for the academic year as well as covering regular graduate tuition.

The UGRF affords Brian the opportunity to pursue his projects full-time during the 2020-21 academic year.
corona virus gettyCongratulations to Tolga Tasdizen whos Emerging COVID-19/SARS-CoV-2 Research Application has been awarded funding by the University of Utah Health’s 3i Initiative.

The project entitled AI/CXR Early Warning System for Infectious Respiratory Disease Outbreaks, proposes to research an early warning system for novel respiratory infectious disease outbreaks based on automated emerging cluster analysis of routine chest x-rays (CXR) using Artificial Intelligence/Machine Learning (AI/ML) and furthermore, to the use data collected during the COVID-19 pandemic to validate our proposed models.

covid visus

SCI Institute and CEDMAV alumnus, Brian Summa has been working with colleagues at Tulane University to study the effects of COVID-19 on lung tissue. This research is made possible using ViSUS to analyze high resolution histological volumes too large to visualize with other software.

GRFP logoCongratulations to Lindsay Rupp who was awarded an NSF Graduate Research Fellowship.and Jake Bergquist who received an honorable mention.

The NSF Graduate Research Fellowship Program (GRFP) helps ensure the vitality of the human resource base of science and engineering in the United States and reinforces its diversity. The program recognizes and supports outstanding graduate students in NSF-supported science, technology, engineering, and mathematics disciplines who are pursuing research-based master's and doctoral degrees at accredited United States institutions.

lorensenThe SCI Institute faculty, staff, and students were shocked and saddened to learn that our great friend and mentor Bill Lorensen passed away on December 12 from complications of colon cancer. Typically for Bill, he was optimistic and good humored to the end.

Bill was a visionary researcher who enthusiastically shared his technical gifts with everyone. He loved thinking and working on interesting problems in visualization and software and found true joy in collaborating with researchers at every level and in every area. Bill’s humor was infectious and he told a great story, especially over an after-work beer, another of Bill’s passions.

chris chuckChris Johnson and Chuck Hansen will be inducted into The IEEE Visualization Academy (or in short Vis Academy) during the opening session of the VIS 2019 conference in Vancouver, BC, on Tuesday, October 22, 2019. The Vis Academy was established in 2018 by the IEEE vgtc Executive Committee, with the inaugural “class” of inductees to include all the Visualization Career Awardees and all the Visualization Technical Achievement Awardees, from 2004 to 2019, for a total of 32 inductees. Induction into the Vis Academy is the highest and most prestigious honor in the field of visualization.