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Research Highlights

April 18, 2017

2016 Image-Based Biomedical Modeling (IBBM) summer course

The Image-Based Biomedical Modeling (IBBM) summer course was held for the third time in 2016, from July 11-21, 2016 in Newpark Resort, Park City (Utah). The two-week course format included the following activities:

Didactic lecture sessions given by the three PIs (Rob MacLeod, Ross Whitaker and Jeff Weiss) as well as three invited instructors (Miriah Meyer, Steve Maas and Gerard Ateshian) experts in their fields… Read more
Jul 11, 2016

Introduction to Image-Based Modeling

Sponsored by the R. Harold Burton Foundation

Over the course of four weeks, students from West High School and Skyline High School and a homeschooled junior year student were given an introduction to image-based modeling (IBM) as part of the SCI Institute Summer Internship. This course, which is given to undergraduate students during the academic year, was customized to fit the high school students' level. The goal… Read more
Jan 12, 2016

Image Analysis Tools for Understanding Connective Tissue Structure

Sponsored by the Burton Foundation This summer, two Salt Lake area high school students from Copper Hills High School came to the University of Utah to participate in a hands-on research experience. The students learned how image analysis tools help biomechanics researchers understand the effects of structural features of musculoskeletal tissues (e.g. tendons, ligaments, and articular cartilage) on the functional… Read more
M Mizargar sm1
Oct 09, 2015

Visualizing Hurricanes

On September 27th, Hurricane Joaquin, a Category 4 storm developed over the Atlantic Ocean pounding the Bahamas. There were a number of predications as to which way the storm would travel, one of which was that the hurricane would head north along the east coast of the United States, but the path of the storm changed direction and dissipated on October 7th.

Knowing the path and strength of a hurricane is vital for… Read more
IMG 4841
Sep 03, 2015

2015 Image-Based Biomedical Modeling (IBBM) summer course

The Image-Based Biomedical Modeling (IBBM) summer course was held July 13- 23 in Newpark, Park City (Utah).

The two-week course included the following activities:
Didactic lecture sessions given by the three PIs as well as four invited instructors and experts in their fields . Laboratory exercises led by a group of 10 teaching assistants and developers. Discussion session time for student-instructor interaction. A… Read more
Aug 20, 2014

2014 Summer Course on Image-based Biomedical Modeling (IBBM)

The Image-Based Biomedical Modeling (IBBM) summer course was held from July 14 to July 24 in the Newpark Hotel, Park City, Utah.
The two-week summer course hosted 39 participants this year: 31 graduate students, 1 MD/PhD student, 2 postdoctoral fellows, 3 junior faculty, and 2 developers from a research laboratory / industry. Participants came from 24 institutions, including 4 from universities in Belgium and… Read more
Aug 12, 2014

Understanding the Morphology of Brain Disorders

This summer, high school students from the Salt Lake area are coming to the University of Utah to participate in hands-on research in image analysis of the human brain. In conjunction with graduate students and faculty in the School of Computing and the Scientific Computing and Imaging Institute, the students are learning how computer science can help neuroscience researchers understand the brain and disorders that… Read more
Jul 29, 2014

Neuro Stimulation

There has been a recent explosion of interest in the use of noninvasive transcranial brain stimulation (or "neurostimulation"), both in clinical settings and as a research tool. One of the two main ways to stimulate the brain transcranially is to run a current to the brain through the magnetic fields generated by a coil that is held near the scalp. This approach has been approved by the FDA for treating depression.… Read more
Jul 29, 2014

SCIRun 5 Development

SCIRun is the integrated programming environment that has been a core technology of the CIBC since its inception and each major version release is an enormous undertaking. The program now contains hundreds of thousands of lines of C++ code and a new release requires at least a review of all this code, with replacement or updating of larger portions of it. We are nearing the first release of such a major new version,… Read more
Jul 29, 2014

Mesh Generation and Cleaver

Figure 1: 3D surface mesh of a face. Partial differential equations (PDEs) are ubiquitous in engineering applications. They mathematically model natural phenomena such as heat conduction, diffusion, and shock wave propagation. They also describe many bioelectrical and biomechanical functions and are a central element of the simulation research of the Center. Analytical solutions for most PDEs are known only for… Read more
May 28, 2014

Evolution of the Medical Classroom

Evolution of the Medical Classroom Introducing ViSOAR As data acquisition advances, and data sizes increase, the need for tools to process and visualize the results in an effective and efficient manner is becoming increasingly important. The reliance on supercomputers for scientific visualization and analysis is already proving to be a hindrance for wide accessibility to researchers and scientists dealing with large… Read more
Dec 19, 2013

Neural Bioelectricity with EGI

In collaboration with Dr. Don Tucker and his colleagues at Electrical Geodesics Inc (EGI) and the University of Oregon, this DBP is concerned with improving our ability to reconstruct and visualize neuroelectric sources (source localization) from EEG measurements and also our ability to stimulate specific brain regions using electrodes attached on to the scalp of the subject (transcranial direct current stimulation,… Read more
Dec 18, 2013

Cam Femoroacetabular Impingement Analysis using Statistical Shape Modeling

Mean control (left) and cam (right) shapes. Middle images show the mean control shape with color plots depicting how the mean cam shape differed across the femoral head, neck, and proximal shaft. Top and bottom rows show different rotations of the femoral head. Volumetric CT images from a cam FAI patient. Validated threshold settings were applied to CT images to segment and reconstruct the bony morphology of each… Read more
Dec 17, 2013

MRI Image Quantification Analysis for Atrial Fibrillation

Corview screenshot Atrial fibrillation (AF) is a cardiac rhythm disturbance in which the atria, the upper chambers of the heart, undergo uncontrolled and uncoordinated electrical activation so that contraction of the atria contributes almost nothing to cardiac output. While not immediately atal (as is ventricular fibrillation) AF dramatically increases the risk of stroke, elevates mortality, and diminishes quality… Read more
DBS figure
Dec 16, 2013

Deep Brain Stimulation Planning with ImageVis3D

Overview of the DBS system. The DBS electrode is implanted in the brain during stereotactic surgery. The electrode is attached via an extension wire to the IPG, which is implanted in the torso. The entire system is subcutaneous and is designed to deliver continuous stimulation for several years at a time. In recent years, there has been significant growth in the use of patient-specific models to predict the effects… Read more
Torso stuff
Dec 16, 2013

New Strategies in Biomedical Mesh Generation

A cross-section of a 3-dimensional, tetrahedral mesh of a torso. Each separate organ type is shown using a different color. This year, an essential goal has been to enhance the generalized image-processing pipeline of software developed by CIBC and its partners. With the growing use of high quality medical imaging, practitioners around the globe are employing these acquired datasets for performing biomedical… Read more
scirun 1
Dec 16, 2013

Software Dissemination at the CIBC

For years, a central focus of the Center for Integrative Biomedical Computing has been software dissemination. Over the Center's twelve-year history, the infrastructure of CIBC's software dissemination efforts have undergone a radical evolution, with many lessons learned for both users and developers.
Software Dissemination as a Form of Science and Technology Dissemination The SCIRun/BioPSE Problem-Solving… Read more
Oct 29, 2013

Today's Tools - Tomorrow's Scientists: An ImageVis3D Project

The SCI Institute holds a strong belief that providing research opportunities to undergraduate and even high school students will not only encourage them to pursue studies in the sciences, but also give them a head start in their future academic lives. Being allowed to work side by side with PhD-level scientists within a real research institute moves science from something that happens in a text book or highly… Read more
Nov 30, 2012

Solving Mysteries of Autism via The Power of Collaboration

Solving Mysteries of Autism via The Power of Collaboration Dr. Guido Gerig Early-Brain Development Research Reveals Vibrant Clues By Peta Owens-Liston
The glossy whiteboards that line the walls in offices, lounge areas, and conference rooms are one of the first things Guido Gerig, PhD, noted when the University of Utah's Scientific Computing and Imaging (SCI) Institute first began courting him to join their team in… Read more
Jun 11, 2012

Mobile Mayhem: Researchers Harness Kraken to Model Explosions via Transport

Mobile Mayhem: Researchers Harness Kraken to Model Explosions via Transport by Gregory Scott Jones - NICS
The crater resulting from the Spanish Fork Detonation. First, the bad news: all across America, trucks and tractor-trailers are transporting industrial explosives on nearly every artery of the country's interstate and highway system. That's right, volatile explosives, including munitions, rocket motors, and… Read more
May 21, 2012

Meshing for Multimaterial Biological Volumes: BioMesh3D

Introduction Figure from R.S. MacLeod, et al., Subjectspecific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples. Example A particle system provides adaptive sampling the various material boundaries of a segmented CT volume from a human torso. Over the past year the CIBC, in partnership with our collaborators, has begun to introduce a generalized… Read more
May 21, 2012

Atrial Fibrillation

Introduction Atrial fibrillation (AF) is an electrophysiological condition that represents an increasing problem in the aging populations of the world; AF doubles the risk of stroke and mortality and diminishes quality of life. The best current method to evaluate the progression of AF and monitor the success of interventions is via an invasive intra-cardiac catheter-based electrical mapping procedure. A noninvasive… Read more
May 21, 2012

Uncertainty Visualization

Introduction An Isosurface visualization of a magnetic resonance imaging data set (in orange) surrounded by a volume rendered region of low opacity (in green) to indicate uncertainty in surface position. The estimation and visualization of uncertainty information is an important research problem in both simulation and visualization. Uncertainty is a term used to describe the error, confidence, and variation of a… Read more
Dec 10, 2010

Imaging Meets Electrophysiology

Atrial fibrillation (AF) is the most common—and perhaps most insidious—form of heart rhythm disturbance and treating it has become the focus of a group of bioengineers, imaging physicists, and physicians at the University of Utah.

In atrial fibrillation, the upper two chambers (the left and right atria) of the heart lose their synchronization and beat erratically and inefficiently. The same condition in the lower… Read more
clearview vishuman1 001
Jul 27, 2010


Figure from T. Fogal and J. Krüger, a Clearview rendering of the visible human male dataset Attempting to display the entirety of a large volumetric dataset at one time would result in an overwhelming amount of information. Furthermore, visualization tools based on volume rendering present the user with a host of confusing options. We present ClearView, which provides a simplified volume visualization tool with a… Read more
Jul 26, 2010

Simulation of Electric Stimulation for Bone Growth

Figure from B.M. Issacson, et al., A unilateral hierarchical model was assembled as a representative image consisting of skin (purple) adipose tissue (yellow), musculature (pink), bone (blue), bone marrow (orange), and internal organs (green) (a). Each tissue type was assigned a specific conductivity using SCIRun. A large serpentine-like mass of HO was identified in the medial aspect of the residual limb, and was… Read more
Jul 26, 2010

Subject Specific, Multiscale Simulation of Electrophysiology

A "typical" workflow that applies to many problems in biomedical simulation contains the following elements: (i) Image acquisition and processing for a tissue, organ or region of interest (imaging and image processing), (ii) Identification of structures, tissues, cells or organelles within the images(image processing and segmentation), (iii) Fitting of geometric surfaces to the boundaries between structures and… Read more
marclab retina
Apr 05, 2008

CRCNS: Fighting Blindness

Despite great advances in neuroscience and medical technology in recent decades, nearly ten million Americans still suffer blindness due to retinal degenerative diseases such as retinitis pigmentosa (RP), age-related macular degeneration (AMD), diabetic retinopathy, and glaucoma. Unfortunately, current treatments available for these conditions are still quite limited. A primary challenge to developing effective… Read more
scirun defibsim
Sep 10, 2007

Developing the Next Generation Tools for Preoperative Planning for Implantable Cardiac Defibrillators

BioPSE visualizing the electrical field generated by an ICD device.

One of the exciting projects in which the SCI Institute is collaborating is the development of new tools and techniques to assist doctors optimize the placement of Implantable Cardiac Defibrillators (ICDs) prior to surgery.

The use of ICDs has greatly increased over the last few years due to their efficacy in preventing sudden cardiac death (SCD) in… Read more
broadman areas
Mar 01, 2007

Building a Better Brain Atlas

Thursday, 01 March 2007 19:51

In 1909 the Broadman areas map was published which localized various functions of cortex.

Since the beginning of the 20th century, scientists have used brain models to study the anatomy and function of the human brain. It was discovered that each part of the brain's anatomy has specific functions for the mind and body. Over the years increasingly sophisticated atlases, or maps of brain… Read more
vistrails vis-spreadsheet1
May 10, 2006

VisTrails: A New Paradigm for Dataflow Management

Modern problem solving environments such as SCIRun have provided scientists with the essential tools for composing complex simulations and visualizations of large scale data. The dataflow programming paradigm has made what was once a rather daunting programming endeavor into a relatively simple point and click process. By condensing the programs into nice little modules that could be visually strung together with… Read more
vessel growth diag
May 05, 2006

The Mechanics of Angiogenesis

Angiogenesis, or the formation of new blood vessels, is a critical part of tissue growth and healing processes. Understanding the underlying mechanisms of this process and how it affects the perfused tissues is fundamental to many issues in medicine. For example, control of angiogenesis could help bones and tissues to heal faster or with better results. In contrast, the inhibition of angiogenesis in some cases could… Read more
May 04, 2006

Embryos Exposed in 3-D

New Method Can Identify What Genes Do, Test Drugs' Safety May 4, 2006 -- Utah and Texas researchers combined miniature medical CT scans with high-tech computer methods to produce detailed three-dimensional images of mouse embryos – an efficient new method to test the safety of medicines and learn how mutant genes cause birth defects or cancer.

"Our method provides a fast, high-quality and inexpensive way to visually… Read more
Feb 08, 2006

The Center for Interactive Ray-Tracing and Photo Realistic Visualization

The SCI Institute is honored to host a new Center of Excellence for Interactive Ray-Tracing and Photo Realistic Visualization dedicated to the development of tools for interactively visualizing large-scale datasets on the fly with advanced lighting and material models that help users understand the subtle detail in high-fidelity datasets. The Center of Excellence program is funded by the state of Utah to accelerate… Read more
visproblems splash
May 05, 2005

Top Scientific Visualization Research Problems

Dr. Christopher R. Johnson
[PDF version]Scientific visualization as currently understood and practiced is still a relatively new discipline. As a result, we visualization researchers are not necessarily accustomed to undertaking the sorts of self-examinations that other scientists routinely undergo in relation to their work. Yet if we are to create a disciplinary culture focused on matters of real scientific… Read more
cervical fig1
Feb 16, 2005

CT Segmentation and 3-D Reconstruction with Morphometric Analysis for Evaluation of Occipital-Cervical Instability in Children

Lindsey J. Healy

Down syndrome is a common chromosomal disorder that affects 0.15 percent of the total population. Individuals with Down syndrome are prone to spinal instability due to congenital abnormalities in the occipital-cervical (O-C1) joint near the base of the skull. To determine the possible abnormality causing this instability, an image-processing pipeline was created by combining several available… Read more
tar creature02
Sep 01, 2004

Level-Set Metamorphosis Goes Hollywood

Associate Professor Ross Whitaker and Assistant Professor David Breen (Drexel University) have been developing surface modeling techniques based on level sets. These techniques include efficient algorithms for representing level-set surfaces and a new formulation for deforming one 3D object into another (also called 3D morphing). This combination of technologies provides an easy and efficient way to smoothly… Read more
vortex fig01
Aug 02, 2004

Visualization of Vortex Flow Structures in Aerodynamics Applications

Dr. Xavier Tricoche

Fig. 1

Computational Fluid Dynamics (CFD) has become an essential tool in various engineering fields. In aeronautics it is a key element in the design of modern aircrafts. The performances of today's computers combined with the increasing complexity of physical models yields numerical simulations that accurately reproduce the flow structures observed in practical experiments and permit to study… Read more
gk tensorfields fig1
Jun 09, 2004

Visualization of Anatomic Covariance Tensor Fields

Gordon L. Kindlmann, David M. Weinstein, Agatha D. Lee, Arthur W. Toga, Paul M. Thompson

The computation, visualization, and interpretation of brain variability remains a significant challenge in computational neuroanatomy. Current deformable registration methods can generate, for each vertex of a polygonal mesh modeling the cortical surface, a distribution of displacement vectors between the individual models and… Read more
isosurface fig1
Jun 09, 2004

Interactive Point Based Isosurface Extraction

Yarden Livnat, Xavier Tricoche

We have proposed a novel point-based approach to view dependent isosurface extraction. We also introduce a fast visibility query system for the view dependent traversal, which exhibits moderate memory requirements. Using this technique, we achieved an interactive interrogation of the full visible woman dataset (1GB) at more then four frames per second on a desktop computer. The… Read more
Jan 10, 2004

BioTensor: Visualizing Diffusion Tensor MRI

Diffusion tensor MRI visualization is a growing field of research. The scanners are collecting better data all the time, and doctors and scientists are constantly discovering new applications for this data. However, unlike scalar and vector data, high-dimensional tensors are not always intuitive to visualize. When devising new strategies for DT-MRI visualization, it is important to understand both what exactly it is… Read more
Jan 08, 2004

Scientific Visualization in Small Animal Imaging

Gordon Kindlmann, Richard A. Normann, Arun Badi, Charles Keller, Greg M. Jones, Christopher R. Johnson

Biomedical applications of small animal imaging are creating exciting opportunities to extend the scientific impact of visualization research. Specifically, the effective pairing of non-linear image filtering and direct volume rendering is one strategy for scientists to quickly explore and understand the volumetric… Read more
Mar 17, 2003

Collaborative Remote Visualization

Jennifer Simpson, Eric luke, MS., Allen Sanderson, Phd. Introduction In the last few years, scientists and researchers have given a great deal of attention to the area of remote visualization of scientific datasets within collaborative environments. This recent interest has been fueled by the use of interactive viewing as the primary means by which researchers explore large datasets. However, researchers often need… Read more
Mar 17, 2003

Undergraduate Research at the SCI Institute

Undergraduate research opportunities at the University of Utah have dramatically increased in the past several years. Positions that were once reserved for graduate students have now been opened up through a variety of programs. The SCI Institute has taken full interest in promoting and co-sponsoring these opportunities--namely, the Engineering Scholars Program and the Access Program for Women in Science and… Read more
star-ray livingroom
Jul 27, 2002

Star-Ray Interactive Ray-Tracer Debuts at SIGGRAPH 2002

Michelangelo's David; a large-scale seismic volume; the moons of Jupiter; four half-full wine glasses; the Greek Parthenon. What do these models have in common? They were all part of the Star-Ray demonstration at SIGGRAPH 2002, held in San Antonio, July 22-24. With support from SGI, researchers from SCI, GDC, VisSim, and the Graphics group designed, implemented, and premiered interactive ray-tracing of a complex… Read more
mri-epi figure-1
Jun 17, 2002

Parametric Method for Correction of Intensity Inhomogeneity in MRI Data

A. Samsonov, R. Whitaker, C.R. Johnson

Intensity inhomogeneity is one of the main obstacles for MRI data post processing. The problem requires retrospective correction due to the strong dependence of the inhomogeneity on patient anatomy and the accompanying acquisition protocol. We have developed a new method for correcting the inhomogeneities using a polynomial estimation of the bias field. The method minimizes the… Read more
dendrite yellow
Sep 28, 2001

Segmenting Tomographic Data

Dr. Ross Whitaker and Vidya Elangovan

Traditionally, processing tomographic data begins with reconstructing volumes. However, when the tomographic data is incomplete, noisy, or misregistered tomographic reconstruction can produce artifacts in the volume, which makes subsequent segmentation and visualization more difficult. Researchers in the SCI institute are developing direct methods for segmenting tomographic data.… Read more
vsc tools
Sep 20, 2001

Immersive Visualization: A Research Update

J.D. Brederson and M. Ikits What is Immersive Visualization? The goal of visualization is to aid in the understanding of complex scientific data, typically using techniques from the fields of computer graphics and animation. To gain additional insight, immersive visualization places the user directly within the data space through virtual reality technology. The resulting immersive experience allows exploration from… Read more
Jul 10, 2001

The Simian Project

By J. Kniss, G. Kindlmann, C. Hansen
This page documents the evolution of our volume rendering project, named Simian. As volume rendering goes, this system is quite a departure from the way this process is typically approached. Most direct volume renderings produced today employ one-dimensional transfer functions, which assign color and opacity to the volume based solely on the single scalar quantity that comprises… Read more
scirun main
Mar 29, 2001

SCIRun/BioPSE: Problem Solving Environments for the Next Generation of Scientific Computing

In March of 2001, the Scientific Computing and Imaging Institute reached a milestone with the long anticipated release of both SCIRun 1.0.0and BioPSE 1.0.0.

"I am excited about the SCIRun and BioPSE software releases," says the Institute's director Christopher R. Johnson. "We have been working on SCIRun since 1992. What started out as software designed by a few people (Steve Parker with help from David Weinstein)… Read more
Jan 22, 2001

The Science and Application of Complex Meshes

Lisa Durbeck Part 1. Unstructured Meshes in Entertainment and Engineering
Tomb Raider

If you have played just about any modern Nintendo(tm) or Playstation (tm) computer game, then you have encountered meshes. Many games make heavy use of what are called polygonal surface meshes, or surfaces built up out of polygons. They are used in the models of many of the people and cars and other 3D things within the game.… Read more
fig1 setup sm
Jan 10, 2001

The Mathematics Behind Imaging

By Oleg Portniaguine.
An interesting, but very challenging kind of imaging is to visualize the interior of a non-transparent object (such as a human body) using physical fields measured outside the body. This imaging is achieved through a mathematical engine known as "inverse problems solving" or "statistical optimization", one of the key research directions at the SCI Institute.

Another research direction being… Read more
Jul 14, 2000

New Methods for Revealing Brain Structure

By Gordon Kindlmann.
The technology of Magnetic Resonance Imaging (MRI) has been used in an ever-increasing variety of applications in the area of medical imaging. This is partly because of MRI's basic ability to non-invasively and non-destructively take images of living tissue, and also because of the inherent flexibility in the way that MRI machines are programmed in order to acquire images. One relatively new… Read more