News

Jake Bergquist Receives HRS Fellowship Award

Congratulations to Jake Bergquist who received the Heart Rhythm Society fellowship award. This is a one year, $50,000 fellowship to support research in cardiac electrophysiology. Read more

Jake Bergquist Presents Two Talks at CinC2022

This year at computing in cardiology I presented two talks, both on the subject of uncertainty quantification in the context of electrocardiographic imaging. Uncertainty quantification is a technique to understand how models such as those we use to simulate or estimate the activity of the heart respond to errors or variability in the inputs to these models. Read more

ShapeWorks 6.3 Now Available

We are excited to announce the new release of our software, ShapeWorks 6.3!

To download installation packages for Windows/Mac/Linux and/or the source code, please visit https://github.com/SCIInstitute/ShapeWorks/releases/tag/v6.3.0

Read more

Brian Zenger receives Outstanding Dissertation Award for 2021

Congratulations to Brian Zenger for receiving the Outstanding Dissertation Award for 2021 from the College of Engineering!

"Experimental Examination of Partial Occlusion Acute Myocardial Ischemia"

Read more

Anna Busatto and Lindsay Rupp Accepted to Simula Summer School in Computational Physiology

Anna Busatto and Lindsay Rupp, PhD students in the Biomedical Engineering Department and the SCI Institute, who study with Dr. Rob MacLeod and the CEG group, were two of the thirty accepted participants for the Simula Summer School in Computational Physiology 2022. This summer-long program is a unique opportunity for graduate students to participate in lectures and projects, first in Oslo, Norway and then in San Diego, CA. A big benefit is the chance to network with mentors and graduate… Read more

U of U Health Professor and SCI Collaborator Receives Pew Charitable Trust Innovation Award

Gabrielle Kardon, Ph.D., a professor of Human Genetics at University of Utah Health, is a recipient of a 2021 Pew Charitable Trust Innovation Award. She is one of 12 accomplished scientists with expertise in molecular biology, genetics, immunology, neuroscience, or other key fields who were selected to investigate critical issues linked to human health. Read more

ShapeWorks 6.2 Now Available

We are excited to announce the new release of our software, ShapeWorks 6.2!

To download installation packages for Windows/Mac/Linux and/or the source code, please visit https://github.com/SCIInstitute/ShapeWorks/releases/tag/v6.2.0

Read more

FluoRender Funded for Another Three Years

FluoRender: Rapid Quantitative Analysis and Adaptive Workflows for Fluorescence Microscopy Data in Fundamental Biomedical Research FluoRender is a software package for interactive visualization and analysis of multichannel and multidimensional fluorescence microscopy data. This project will continue to serve the pressing needs of biologists utilizing fluorescence microscopy for flexible and reliable data analysis. FluoRender also addresses the problems in fundamental biomedical research that… Read more

ShapeWorks 6.1 Now Available

We are excited to announce the new release of our software, ShapeWorks 6.1!

To download installation packages for Windows/Mac/Linux and/or the source code, please visit https://github.com/SCIInstitute/ShapeWorks/releases/tag/v6.1.0 Read more

ShapeWorks 6.0 Released

We are excited to announce the new release of our software, ShapeWorks 6.0!

To download installation packages for Windows/Mac/Linux and/or the source code, please visit https://github.com/SCIInstitute/ShapeWorks/releases/tag/v6.0.0 Read more

SCI Institute and Kitware: Putting Software Sustainability into Practice

Authors:

SCI Institute, University of Utah: Jess Tate, Daniel White, Alexandra Warner, Ross Whitaker, Christopher Johnson, Rob MacLeod

Kitware: Will Schroeder, Jean-Christophe Fillion-Robin, Dženan Zukić, Matt McCormick, and Lee Newberg

Story originally appears on the Kitware Blog

ShapeWorks 5.5 Released

We are excited to announce the new release of our software, ShapeWorks 5.5!

To download installation packages for Windows/Mac/Linux and/or the source code, please visit https://github.com/SCIInstitute/ShapeWorks/releases/tag/v5.5.0

ShapeWorks Users Get-togethers: We have been maintaining a monthly, remote get-together for ShapeWorks users that is alternating between software-centric, demonstrating new/improved software features, and user-centric meetings, with open discussions that include Q&A,… Read more

Wilson Good Wins Young Investigator's Award at Computing in Cardiology

Congratulations to Wilson Good on winning the Rosanna Degani Young Investigators’ Award competition at the international Computing in Cardiology conference, Rimini, 16th September 2020. Read more

ShapeWorks 5.4 Released

We 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 Read more

Brian Zenger Receives University of Utah Graduate Fellowship

Congradulations 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. Read more

SCI Students Awarded One NSF Graduate Research Fellowship and One Honorable Mention

Congratulations 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… Read more

SCI mourns the passing of friend and mentor Bill Lorensen

The 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… Read more

DBS and Traumatic Brain Injury

Biomedical engineers in the laboratory of Christopher R. Butson, PhD at the Scientific Computing & Imaging (SCI) Institute are part of a team currently investigating the use of deep brain stimulation (DBS) to treat patients suffering from traumatic brain injury. The goal of this investigational therapy is to restore function through electrical stimulation. The first subject in this trial study is a woman who suffered a traumatic brain injury as the result of a car accident 18 years ago. Since… Read more

SCI Head Model Now Available

The SCI Institute is excited to announce the release of the SCI Institute's female head and brain model data repository and pipeline.

The dataset and corresponding publication can be found here. Read more

Trayanova Predicting Ablation Targets 2 pyramid

3D Virtual Simulation Gets to the ‘Heart’ of Irregular Heartbeats

Researchers have successfully performed 3D personalized virtual simulations of the heart

A 3-D virtual heart. Credit: Johns Hopkins University Read more

Machine learning could improve how doctors diagnose heart attacks

Wilson Good, Brian Zenger
Article originally appears in Venturebeat

You're working in your house, going about your normal routine when suddenly the pain hits. Your chest starts to throb and your left arm begins to ache. Without hesitation, you rush to the hospital, dreading your worst fear has become a reality — you are having a heart attack. Upon arrival, physicians, nurses, and other medical staff begin frantically testing, probing, and prodding nearly every part of your body. They run more… Read more

Rob MacLeod elected President of the Board of Directors for the Computing in Cardiology Society

Scientific Computing and Imaging (SCI) Institute faculty member Rob MacLeod has been elected as President of the Board of Directors for the Computing in Cardiology Society for the next three years. Read more

Snapshots of Life: Muscling in on Development

Research with Fluorender highlighted on the NIH Director's Blog.
Posted on July 27, 2017 by Dr. Francis Collins

Twice a week, I do an hour of weight training to maintain muscle strength and tone. Millions of Americans do the same, and there's always a lot of attention paid to those upper arm muscles—the biceps and triceps. Less appreciated is another arm muscle that pumps right along during workouts: the brachialis. This muscle—located under the biceps—helps your elbow flex when you are doing all… Read more

Research Initiative Seeks to Understand Neural Pathways in Deep Brain Stimulation

The University of Utah Neuroscience Initiative recently announced Christopher Butson, PhD, Associate Professor in Bioengineering and the Scientific Computing and Imaging Institute, was awarded funding for his project, "Differentiating Neural Circuits Modulated During Therapeutic Versus Ineffective Deep Brain Stimulation". Read more

Rob MacLeod Elected as a Fellow of the American Institute for Medical and Biological Engineering (AIMBE)

Congratulations to Rob MacLeod for being elected a Fellow of the American Institute for Medical and Biological Engineering (AIMBE). After very careful consideration, including the most rigorous and selective review process in AIMBE's history, Rob was among an impressive group who were elected to the 2017 Class of the College of Fellows. Read more

SCIx 2016: November 16th

SCI Institute Technical Exchange (SCI X) was created to strengthen the interactions between the SCI Institute and other academic researchers, and also those companies conducting or wishing to conduct research with the University and inspire them to increase their collaborative efforts in research and new product development.

SCI X is intended to provide its guests access to unique resources and expertise found within the SCI Institute, creating an expanded relationship between the SCI Institute… Read more

Fluorender Features on Cover of Disease Models and Mechanisms

An image of the ulnar-mammary syndrome, visualized with FluoRender, was chosen for the cover of Disease Models and Mechanisms. CIBC Collaborator, Gabrielle Kardon's article can be found here in it's entirety.

Development of a subset of forelimb muscles and their attachment sites requires the ulnar-mammary syndrome gene Tbx3.
Mary P. Colasanto, Shai Eyal, Payam Mohassel, Michael Bamshad, Carsten G. Bonnemann, Elazar Zelzer, Anne M. Moon, Gabrielle Kardon Read more

Fluorender 2.20 Released

We are excited to announce the latest release of FluoRender, version 2.20, which incorporates improvements, bug fixes, and new features.

You can download FluoRender here

New Features:

Clustering algorithms. Three clustering algorithms for segmentation are added: expectation-maximization on Gaussian mixture, DBSCAN, and k-means. Users can use these methods in the "Component" window. Improved tracking algorithms. Tracking accuracy has been improved. We improved the algorithm for generating the… Read more

Alex Lex, Bei Wang Phillips, and Chris Johnson present at the Future in Review Conference

Alex Lex, Bei Wang Phillips, and Chris Johnson were chosen to present at the Future in Review Conference held at the Stein Eriksen Lodge in Park City, Utah.

What is Future in Review? Hosted by Mark Anderson, founder and publisher of the Strategic News Service™, the Future in Review® (FiRe) conference exposes world experts and participants to new ideas in a manner that produces an accurate portrait of the future in technology, including the global economy, cloud computing, biology and medical… Read more

Scientific visualizations: A bridge to knowledge

Chris Johnson speaks with ScienceNode on visualizations as a collaborative process of discovery, and a crucial step on path to knowledge.

Read the full article here. Read more

Fluorender 2.19.4 Available

We are excited to announce the latest release of FluoRender, version 2.19.4, which incorporates improvements, bug fixes, and new features.

Download FluoRender

In this release, we mainly improved the usability of a series of functions for 4D analysis, including the component analyzer, 4D scripts, paint brush tools, and format supports. We have also made a series of video tutorials and published them on YouTube.
Read more

NeuroImage Journal Cover Features SCIRun Renderings

The publication and cover image is the result of a close collaboration between the University of Freiburg (Lukas Fiederer, Tonio Ball and others) in Germany and the NIH-funded Center for Integrated Biomedical Computing (CIBC, Moritz Dannhauer) at the SCI institute (Johannes Vorwerk). The cover of NeuroImage' March (128) issue illustrates different tissues in a model of the human head that are known to have distinct electrical properties. In this study, we simulated the electrical effect of… Read more

Chris Johnson Re-Elected to CRA Board of Directors

Congratulations to Chris Johnson on being re-elected for another three years to the Computing Research Association board of directors.

You can read the full release here. Read more

Seg3D 2.3.0 Released

We are pleased to announce Seg3D version 2.3.0.

The new binary installers and sources can be downloaded from:
https://github.com/SCIInstitute/Seg3D/releases Read more

Behind Each Breath, an Underappreciated Muscle

CIBC collaborator Gabrielle Kardon's research has been showcased by New York Times science writer Carl Zimmer.

You can read the full article on their website. Read more

Ross Whitaker Elected to AIMBE's College of Fellows

Congratulations to Ross Whitaker, who has been elected to the American Institute for Medical and Biological Engineering (AIMBE) College of Fellows. The AIMBE College of Fellows represents the most accomplished and distinguished medical and biological engineers responsible for innovation and discovery. Read more

Three Grants, Totaling Over $10 Million Awarded to Prof. Chris Butson and Collaborators

Over $10 Million in grants from three federal organizations have been awarded to Christopher R. Butson, PhD, associate professor of bioengineering and a member of the Scientific Computing and Imaging Institute (SCI). He also holds positions in the departments of neurology and neurosurgery and is the Director of Neuromodulation Research for the Department of Neurosurgery and works with teams of researchers at the University of Utah and other institutions in the U.S. and Germany.

The National… Read more

NSF Highlights Chris Butson's New Grant

Press Release 15-107
Gigabit application prototypes to help cities and communities serve citizens better NSF awards nearly $12 million to expand innovation ecosystem for next-generation Internet applications

NSF announced nearly $12 million awards that build on the successful efforts of US Ignite.
Credit and Larger Version September 14, 2015

The United States lags behind most developed countries in terms of high-speed Internet availability. Though there are signs this is changing, insufficient… Read more

CIBC Renewed for Another Five Years

The U's Center for Integrative Biomedical Computing just landed a $6.1 million grant renewal from the National Institutes of Health. The center produces open-source software for image-based modeling, simulation and visualization of biomedical data. Tens of thousands of scientists have downloaded the center's software tools and data sets, and more than 200 papers published by scientists outside the center reference its software or computing infrastructure.

The NIH grant has a five year term. The… Read more

CIBC launces the new NIH BTRPortal

The NIH Center for Integrative Biomedical Computing (CIBC) is pleased to release the National Institutes of Health Biomedical Technology Resource Portal (NIH BTRPortal). The NIH BTRPortal maintains profiles for all National Institute of General Medical Sciences (NIGMS) and National Institute of Biomedical Imaging and Bioengineering (NIBIB) P41 Centers and provides central access to resources developed at these Centers. Recent participation has grown this repository to over 200 software packages… Read more

SCIRun 5.0 Released

The Scientific Computing and Imaging Institute is excited to announce the first official alpha release of SCIRun 5.0!

New features include a new user interface based on the cross-platform Qt toolkit, updated graphics and visualization system, improved algorithm stability, expanded test coverage, a leaner and modernized codebase, better math library support through Eigen, and streamlined support for new modules and toolkit development. A Python scripting engine and Matlab interface will be… Read more

Seg3D 2.2.0 Now Available

We are pleased to announce Seg3D version 2.2.0 and Seg3D's new GitHub repository (https://github.com/SCIInstitute/Seg3D).

The new binary installers and sources can be downloaded from:

http://www.sci.utah.edu/download/seg3d

For users building from source, please review the updated build instructions at www.seg3d.org as our CMake-based build has changed considerably since 2.1.5. This release contains bug fixes, upgraded third party libraries and tool improvements.

As we want to keep improving our… Read more

BrainStimulator Released with SCIRun5 alpha

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).

Its modular implementation builds upon the new release of SCIRun 5.0 and following release versions. No additional software is needed to set up, compute, visualize and analyze simulations and their results. The BrainStimulator-specific modules can be visually and functionally combined to form… Read more

FluoRender 2.16 Released

We are excited to announce the 2.16 release of FluoRender. For Microsoft Windows users, FluoRender 2.16 incorporates minor feature improvements and issue fixes. However, we have upgraded all graphics functions, conforming to the OpenGL core profile specifications. It allows us to have continuous support for future graphics processing units. FluoRender 2.16 requires graphics cards with a minimum support of OpenGL 3.3. Older graphics hardware need to be replaced. For Apple Mac OS X users, there… Read more

SC15 Video Highlights Cutting-Edge Brain Simulations that help Parkinson’s Patients

An enlightening video series launched by the SC conference steering committee in 2013 aims to illustrate how high performance computing is impacting everyday life – from manufacturing to storm prediction to the making of Hollywood blockbusters. The latest in the series is a short video highlighting the innovative work being done at the University of Utah's Scientific Computing and Imaging Institute in regards to helping Parkinson's patients lead more normal lives through deep brain stimulation… Read more

Treating Tremors

Dr. Christopher Butson Interviewed for AMS It may not sound like much fun having an electrode implanted in your brain, yet it's much better than not being able to hold anything even for a second, which can happen to someone with Parkinson's disease or essential tremor. Deep brain stimulation is effective in treating these conditions, but determining the proper stimulating parameters can take many hours and can require multiple visits by patients. Mathematics is part of a new approach that… Read more

Now Available: Scientific Visualization

Edited by Hansen, C.D., Chen, M., Johnson, C.R., Kaufman, A.E., Hagen, H.

Based on a seminar that took place in Dagstuhl, Germany, this contributed volume studies four important topics within scientific visualization: uncertainty visualization, multifield visualization, biomedical visualization and scalable visualization.

Uncertainty visualization deals with uncertain data from simulations or sampled data, uncertainty due to the mathematical processes operating on the data, and uncertainty in… Read more

Chris Butson Joins the SCI Institute as an Associate Professor of Bioengineering

Dr. Butson received a B.S. in Mechanical Engineering from the University of Maryland, M.S. in Electrical Engineering from George Washington University and Ph.D. in Biomedical Engineering from the University of Utah. He completed post- doctoral training at the Cleveland Clinic and for the last six years has been a member of the Biotechnology & Bioengineering Center at the Medical College of Wisconsin (MCW) where he was an Associate Professor in the Departments of Neurology, Neurosurgery,… Read more

Kedar Aras Wins Young Investigator Competition

Congratulations to Kedar Aras who won the Young Investigator prize at the 39th Annual International Society for Computerized Electrocardiology (ISCE) conference on April 29th. Judges evaluated finalist presentations based on the originality of the science, quality of the study, and the clarity of the presentation and Q&A. Each speaker was given 15 minutes for their presentation followed by a 15 minute Q&A session. Read more

Chris Johnson and Ross Whitaker Elected IEEE Fellows

Congratulations 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. Read more

Chris Johnson Receives Sidney Fernbach Award

Congratulations 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… Read more

SCIRun 4.7 with BioMesh3D Released

The 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. Read more

Ross Whitaker Selected Member of CRA CCC

Congratulations 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 http://www.cra.org/ccc/about Read more

Chris Johnson Elected to CRA Board of Directors

SCI 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:… Read more

Cleaver v1.5 Released

The 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. Read more

ImageVis3D 3.0.0 Released

The ImageVis3D team is proud to announce the release of ImageVis3D 3.0.0! ImageVis3D is a desktop volume rendering application which was designed to visualize large data. Support is available for multiple rendering modes, such as 1D and 2D transfer functions, isosurface rendering, as well as specialized modes such as MIP and slice views. On modern systems, ImageVis3D's GPU-accelerated rendering delivers incredible performance, while compatibility options exist to allow ImageVis3D to perform… Read more

CIBC and ImageVis3D Mobile Recognized in List of Important Events in NCRR History

Among the list of important events in NCRR history published in the NIH Almanac is the release of the ImageVis3D Mobile visualization app developed under the CIBC. In the events listed for the year 2010 it states:

"Researchers led by Chris Johnson at the University of Utah's NCRR-supported Center for Integrative Biomedical Computing developed an iPhone application that is changing how and where doctors practice medicine. The ImageVis3D Mobile visualization program enables them to retrieve and… Read more

Best Paper Awarded at MICCAI 2012

Congratulations to Suyash Awate, Peihong Zhu and Ross Whitaker whose paper has been awarded "Best Paper" at the MICCAI workshop on Multimodal Brain Image Analysis. Winning papers are chosen by the organisers based on relevance, novelty and scientific contribution.

S.P. Awate, P. Zhu, R.T. Whitaker. "How Many Templates Does It Take for a Good Segmentation?: Error Analysis in Multiatlas Segmentation as a Function of Database Size," In Int. Workshop Multimodal Brain Image Analysis (MBIA) at Int.… Read more

ImageVis3D 2.1.1 and Mobile Universal 4.0 Released

The ImageVis3D team is proud to announce the release of ImageVis3D 2.1.1.

DOWNLOAD NOW

ImageVis3D is a desktop volume rendering application which was designed to visualize large data. Support is available for multiple rendering modes, such as 1D and 2D transfer functions, isosurface rendering, as well as specialized modes such as MIP and slice views. On modern systems, ImageVis3D's GPU-accelerated rendering delivers incredible performance, while compatibility options exist to allow ImageVis3D… Read more

SCIRun 4.6 with BioMesh3D Released

The SCIRun development team is pleased to announce the release of SCIRun 4.6 with meshing tools. SCIRun 4.6 is available as a binary download for Windows and OS X, and as a source download for Linux.

Download Now

See also the Release notes.
Read more

Visualizing the Future of Medicine

CIBC Software freatures prominently in Scientific Computing World's interview of Chris Johnson "Visualizing the Future of Medicine."
See: Scientific Computing World - "Visualizing the Future of Medicine" (pdf version) Read more

CARMA Team Hosts Successful Atrial Fibrillation Symposium

The Western Atrial Fibrillation Symposium is a comprehensive education meeting focused exclusively on atrial fibrillation. The conference features distinguished faculty and physicians from eight countries and 20 renowned clinical and research centers across the United States.

The symposium has grown greatly since it's origination in 2007. This year's symposium hosted over 300 scientists from around the world. The success of the symposium is due in large part to the hard work and dedication of… Read more

SCIRun 4.5 with BioMesh3D Released

The SCIRun development team are pleased to announce the release of SCIRun 4.5 with meshing tools. SCIRun 4.5 is available as a binary download for Windows and OS X, and as a source download for Linux.

Download

Release notes

Read more

ImageVis3D Mobile 3.0 Released

The ImageVis3D development team is proud to announce the release of ImageVis3D (IV3D) Mobile 3.0! IV3D Mobile is a mobile visualization application designed to visualize and share volume and surface data while you are on the go. With ImageVis3D (available for free at www.imagevis3d.com) and ImageVis3D Mobile you can transfer your own data directly from the desktop to your mobile device. ImageVis3D supports all iPads, iPod touches and iPhones (older devices have a more limited feature set).… Read more

ImageVis3D 2.0 Released

The ImageVis3D team is proud to announce the release of ImageVis3D 2.0. Download ImageVis3D is a desktop volume rendering application which was designed to visualize large data. Support is available for multiple rendering modes, such as 1D and 2D transfer functions, isosurface rendering, as well as specialized modes such as MIP and slice views. On modern systems, ImageVis3D's GPU-accelerated rendering delivers incredible performance, while compatibility options exist to allow ImageVis3D to… Read more

CARMA Collaborator Dr. Nassir Marrouche Profiled in Continuum

CIBC collaborator Dr. Nassir Marrouche is profiled in the Spring 2011 issue of the Continuum.

Creating Good CARMA: Cardiologist Nassir Marrouche Knows Matters of the Heart Read more

CARMA Team Receives Utah Innovation Award

Congratulations to Rob MacLeod, Nassir Marrouche and the CARMA Team who have recently received the Utah Innovaton Award. Read more

Announcing Seg3D 2.0

We are pleased to announce the next generation Seg3D. Version 2.0 features a new more user-friendly interface, better session and project management, many new filters, and many more improvements to ensure stability. Although most of the functionality from the old version has been ported to this new version, some features like volume rendering are scheduled for the next release, version 2.1. The new version of Seg3D is available in binary format for Windows and OS X. Although a 32 bit version… Read more

ImageVis3D Mobile Universal 2.0 Released

ImageVis3D developers are pleased to announce the release of ImageVis3D Mobile Universal 2.0.

It is available from the Apple iTunes App Store. Read more

Rob MacLeod and Nassir Marrouche Interviewed in Pictures of the Future

Dr. Robert MacLeod and Dr. Nassir F. Marrouche are interviewed on their atrial fibrillation research in the Fall 2010 issue of Pictures of the Future. See: "A Strike Against Stroke" Read more

Chris Johnson Honored with 2010 Visualization Career Award

CHRIS JOHNSON, director of the University of Utah’s Scientific Computing and Imaging Institute, has been honored with the 2010 Visualization Career Award. The award was made in Salt Lake City on Oct. 27, 2010 during VisWeek2010, the premier forum for computer visualization researchers. It is sponsored by IEEE, the Institute of Electrical and Electronics Engineers. Johnson’s award was bestowed by the IEEE’s Visualization and Graphics Technical Committee, which honored him for “sustained… Read more

"Best Paper" Awarded at International Meshing Roundtable

Congratulations to Jonathan Bronson, Joshua Levine, and Ross Whitaker whose paper received the Best Paper Award at the 19th International Meshing Roundtable in Chattanooga Tennessee this October.

Jonathan R. Bronson, Joshua A. Levine, and Ross T. Whitaker. "Particle Systems for Adaptive, Isotropic Meshing of CAD Models". In Proceedings of the 19th International Meshing Roundtable, Chattanooga, TN, Oct., pp. (to appear). 2010.

Read more

CIBC Research Spotlighted in NCRR Reporter

Research at the Center for Integrative Biomedical Computing (CIBC) was highlighted as a "Visualizing Success" example in the Winter issue of NCRR Reporter, 2010. See "Recovery Act Funds Fuel Innovative Research Collaborations." Also, in the same issue, the CIBC's iPhone app for ImageVis3D is profiled. See: "NCRR Grantee Creates iPhone Application." Read more

Announcing SCIRun 4.4 with BioMesh3D

The SCIRun development team is pleased to announce the completion of SCIRun 4.4 with meshing tools. SCIRun 4.4 is available as a binary download for Windows and OS X and as a source download for Linux. The new binaries and source tar archives can be downloaded from our Software page. Read more

2010 Rosenblatt Prize Awarded to Computer Scientist and Director of SCI Institute

May 7, 2010 -- Christopher R. Johnson, distinguished professor of computer science and director of the Scientific Computing and Imaging (SCI) Institute at the University of Utah, was honored at today's university commencement ceremonies with the Rosenblatt Prize for Excellence, the U's most prestigious award. The $40,000 gift is presented annually to a faculty member who displays excellence in teaching, research and administrative efforts. The Rosenblatt Prize Committee, a group of… Read more

ImageVis3D Mobile Goes Nuclear

SALT LAKE CITY -- The future of computers is here, and University of Utah scientists keep pushing the envelope. They have developed new imaging programs that turn complex data into brilliant pictures you can view on your iPhone or iPad.

ImageVis3D Mobile became available last fall, and new applications are emerging. The latest is an app that simulates a nuclear reaction.

The colorful, clear, 3-D images are created by ImageVis3D. The program takes abstract phenomena and data and turns it into… Read more

ImageVis3D Mobile iPhone App Hits the News

The release of ImageVis3D Mobile for the iPhone has received wide coverage.
In addition to a news story on KSL channel 5, it has generated a number of print articles such as:

The Daily Utah Chronicle:
"U researchers develop iPhone applications"
Read more

Tom Fogal and Jens Krüger's work on "ClearView" profiled on German ScienceBlogs.

See full story on ScienceBlogs. Read more

Chris Johnson Awarded Cyber Pioneer Award

Chris Johnson, director of the Scientific Computing and Imaging Institute, will receive the prestigious Cyber Pioneer Award. Alan Hall, chair of the Utah Technology Council, will present the award at the 2009 Utah Cyber Symposium on September 25th. The award is designed to honor individuals who are pioneers in Utah’s high tech industry. Read more

ImageVis3D Mobile now available

ImageVis3D Mobile for the iPhone is now available from Apple iTunes App store. Read more

ImageVis3D Released

The ImageVis3D team is proud to announce the release of ImageVis3D 1.0!

ImageVis3D is a desktop volume rendering application which was designed to visualize large data. Support is available for multiple rendering modes, such as 1D and 2D transfer functions, isosurface rendering, as well as specialized modes such as MIP and slice views. On modern systems, ImageVis3D's GPU-accelerated rendering delivers incredible performance, while compatibility options exist to allow ImageVis3D to perform… Read more

Introducing ShapeWorks

The 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… Read more

Chris Johnson Selected as SIAM Fellow

SCI 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… Read more

Chris Johnson and Ross Whitaker Present at the Library of Congress "Computing Research that Changed the World"

Chris Johnson - "Computing and Visualizing the Future of Medicine" (video not available)
Ross Whitaker - "Scientific Computing and Visualization for Medical Image Analysis"

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SCIRun Version 4.0 Released

The 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… Read more

Imaging Meets Electrophysiology

By 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… Read more

map3d 6.5 Now Available

The Scientific Computing and Imaging Institute and the Center for Integrative Biomedical Computing are proud to announce the release of map3d version 6.5!

This release includes a number of fixes and additions to the display settings for map3d and major new support for displaying time fiducials. The driving application for this was displaying maps of activation, recovery, start of QRS, etc., both as separate isochronal maps and superimposed on the scalar time series data. If you need this, you… Read more

CIBC Collaborator Mario Capecchi Wins Nobel Prize

The NIH Center for Integrative Biomedical Computing (CIBC) and the Scientific Computing and Imaging (SCI) Institute would like to join the international scientific community in extending our heartiest congratulations to our University of Utah colleague Dr. Mario Capecchi as one of the three recipients of the 2007 Nobel Prize in Physiology or Medicine. This award recognizes the ground-breaking work of Dr. Capecchi and his scientific contemporaries, Dr. Oliver Smithies of Cardiff University in… Read more

SCIRun Meets CCA: SCIJump Released for Testing

SCIJump is a computational environment or framework based on the Common Component Architecture (CCA) standard for high performance component frameworks in the scientific computing domain. The SCIJump framework builds on the SCI Institute's SCIRun Problem Solving Environment and implements a parallel component and distributed computation architecture which can support a diverse set of component- based technologies. Read more

Announcing SCIRun/BioPSE 3.0

BioPSE network computing the effects of electrode placement on the electrical field in the heart and hence evaluating the defibrillation threshold. The Scientific Computing and Imaging (SCI) Institute and the Center for Integrative Biomedical Computing (CIBC) are proud to announce the first major release under the new center of their flagship software SCIRun/BioPSE Version 3.0!

The Biomedical Problem Solving Environment, or BioPSE, contains a suite of applications and integrated problem solving… Read more

The Center for Integrative Biomedical Computing

SCI is pleased to announce the launch of our new NCRR Center for Integrative Biomedical Computing (CIBC), a five year extension of our previous NCRR center but with a new broader scope. With the new center, we will be conducting exciting research and development that builds upon the successes of previous investments, enhancing our existing strengths, and responding to a set of compelling new biomedical problems. We will continue to develop integrated problem solving environments that make… Read more

SCIRun/BioPSE 1.24.2 Now Available

Thanks to everyone for their feedback on the 1.24.0-beta pre-release. Based on your suggestions, we fixed important bugs over the past few weeks, and we added many great new features as well.

This version of SCIRun/BioPSE contains a new PowerApp called "BioImage" for the processing and visualization of medical image volumes. With BioImage users can directly load a variety of native data formats (e.g. DICOM, Analyze, VFF, NRRD, PICT) and can apply processing algorithms to specify and enhance… Read more

SCIRun ported to SGI Prism

The SCI Institute is proud to announce the availability of SCIRun on the Silicon Graphics PrismTM visualization system. The combination of large memory, parallel CPUs and advanced graphics capabilities on the Silicon Graphics Prism provide an ideal platform for the SCIRun problem solving environment. The modular nature of the Silicon Graphics Prism allows scaling to meet the computational needs of the most demanding SCIRun users.

Using SCIRun's advanced volume rendering PowerApp 'BioImage' we… Read more

Chris Johnson Elected Fellow of the American Association for the Advancement of Science

Chris Johnson, a distinguished professor of computer science and director of the Scientific Computing and Imaging Institute, has been elected by his peers as a fellow in the American Association for the Advancement of Science. Johnson is one of 376 AAAS members who were given the distinction this year "because of their efforts toward advancing science applications that are deemed scientifically or socially distinguished," the group says. Johnson specifically was cited "for distinguished… Read more

Chris Johnson Testifies Before Senate Sub-Committee

Chris Johnson, SCI Institute director, testified June 23rd on Capitol Hill before the Congressional Biomedical Research Caucus. His presentation, "Computing the Future of Biomedicine," had a very large turnout, with more than 90 Senate and Congressional Staffers, NIH, NSF and other funding agencies staff, and Congressmen in attendance.

Rush Holt (Rep. New Jersey) followed up Johnson's presentation with a plea for more funding for fundamental research. Read more

SCI Annouces Certificate Program for Computational Bioimaging

The SCI Institute announces a new graduate level certificate program for Computational Bioimaging. The creation of this multidisciplinary program, involving four academic departments, was funded by the Program for Computational Functional Imaging and Visualization through the NIH/NLBI Biomedical Information Science and Technology Initiative (BISTI). The certificate is considered similar to a Graduate Minor at other universities. Graduate students in the program take classes and fulfill the… Read more

Dr. Johnson Gives Frontiers of Science Lecture

Dr. Chris Johnson presented a lecture entitled "Computing the Future of Biomedicine" as part of the University of Utah College of Science's Frontiers of Science Lecture series on March 10. In it he discussed the direction of research in Scientific Computing for medicine and some of the great research going on at SCI. The lecture was held at the Aline Wilmot Skaggs Biology Building. Read more

Chris Johnson Receives Distinguished Professor Award

SCI Institute Director Chris Johnson was recently promoted to the rank of Distinguished Professor of Computer Science. Professor Johnson's research through the years has focused on biomedical computing, visualization, inverse problems and problem solving environments. It is his continuing goal to use his work in scientific computing to create new techniques, tools, and systems, to solve problems affecting various aspects of human life. Read more

SCI Institute Plays Role In Governor's State of the State

For four-year-old Natalie Wright, appearing in front of the state legislature might be just another exciting trip with her family. But, for Governor Mike Leavitt, Natalie represents the fundamental reason for leveraging research and technology within the state of Utah.

Natalie was diagnosed with a brain tumor when she was two years old. Natalie's neurosurgeon knew they had to operate. Natalie's father, John Wright, and neurosurgeon, Dr. Jack Walker called upon the SCI Institute to provide an… Read more

map3d 5.2 now Available

map3d is a scientific visualization application developed at the Nora Eccles Harrison Cardiovascular Research and Training (CVRTI) and the Scientific Computing and Imaging Institute (SCI) at the University of Utah. The original purpose of the program was to interactively view scalar fields of electric potentials from measurements and simulations in cardiac electrophysiology. Its present utility is much broader but continues to focus on viewing three-dimensional distributions of scalar values… Read more

CIBC News

News from the Center for Integrative Biomedical Computing