SCIENTIFIC COMPUTING AND IMAGING INSTITUTE
at the University of Utah

Created: 26 July 2010

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 regions (geometric modelling), (iv) Generation of three-dimensional volume mesh from hexahedra or tetrahedra (meshing), and (v) Application of tissue parameters and boundary conditions and computation of spatial distribution of scalar, vector or tensor quantities of interest (simulation).

Over the past year the CIBC, in partnership with our collaborators, has begun to introduce a generalized processing pipeline and associated software to the biomedical community. This work has been largely influenced by DBP collaborators such as those collaborating to develop optimization strategies for ICD placement in children; Dr. John Triedman at the Department of Cardiology, Children's Hospital Boston, Dr. Matthew Jolley, Stanford University Medical Center. and Drs. Elizabeth Saarel, Tom Pilcher, and Michael Puchalski, all from the Department of Cardiology at Primary Childrens' Hospital in Salt Lake City. Additionally, collaborative work with the goal of the making osseointegrated amputee implants part of an electrical system to accelerate skeletal attachment also influenced the creation of the pipeline described below; collaborators are Brad Isaacson, Dr. Joseph Webster, Dr. James Beck, and Dr. Roy Bloebaum from the Department of Veteran Affairs and University of Utah.

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Created: 30 November 2012

Dr. Guido Gerig Early-Brain Development Research Reveals Vibrant Clues

By Peta Owens-Liston

Dr. Guido Gerig

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 2007. For someone so prominent worldwide for his image analysis expertise and seminal research, whiteboards seemed the simplest of visual tools. Yet, what these signaled to Gerig was that this place fostered collaboration among students, postdocs, and faculty; these ubiquitous boards were an immediate means to visually improve understanding and share knowledge.

Pencil in hand, Gerig fills three pages with a whirl of sketches as he explains how his imaging work illuminates clinical findings in his research involving early brain development, and more specifically autism. The sketches fade to stick figure-status as Gerig jumps back and forth between the paper and the color-exploding images on his computer screen. Vivid and seemingly pulsating with life, the brain-development images are a result of thousands of highly precise, quantifiable measurements never before captured visually.

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Created: 01 September 2004

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 transform any 3D object to the shape of a target form. Recently, these methods were adopted by the special effects gurus at Frantic Films to create stunning visual effects for the movie Scooby-Doo 2.

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