Center for Integrative Biomedical Computing

Center for Integrative Biomedical Computing

University of Utah 72 South Central Campus Drive, Room 3750 WEB Salt Lake City, UT 84112 www.sci.utah.edu/cibc Grant No. P41 RR012553

Principal Investigator Chris R. Johnson, Ph.D. 801-581-7705; Fax: 801-585-6513 C0-Director Rob S. MacLeod, Ph.D. 801-585-7596; Fax: 801-585-6513 Co-Director Ross T. Whitaker, Ph.D. 801-587-9549; Fax: 801-585-6513 Additional Contact Greg Jones 801-587-9825; Fax: 801-585-6513

Research Emphasis

The overall goal of the Center for Integrative Biomedical Computing (CIBC) is to develop integrated problem-solving environments that make advanced computational tools available to biomedical scientists. The specific core areas of interest are image processing and geometric modeling, simulation, and visualization. The center also pursues advanced research in technical and biophysical approaches to electrophysiology and bioelectric field problems in cardiology and neurology.

Current Research

The focus of research within the CIBC is to develop new approaches to solving problems in image processing; visualization of scalar, vector, and tensor fields; and simulation of electrophysiology and bioelectric fields from the heart and brain.

Resource Capabilities

Methods

The resource methods are organized by cores, with one core dedicated to each of image processing and geometric modeling, simulations, visualization, and integrated software environments. Within each core, several computational methods either have been implemented or are in the process of being developed.

Instruments

None. The center provides software to the biomedical research community.

Software

The main focus of the center is the research and development of state-of-the-art software for image processing and geometric modeling, simulation, and visualization, including not just individual tools but also integrative problem-solving environments. The target domains for this software are a variety of biomedical research areas that span a wide range of scales, from subcellular to whole organisms. Specific applications include bioelectric fields, genetics, and feature characterization from medical images. Specific software tools, organized by core areas, include the following:

Image processing and geometric modeling tools: The center is developing powerful and novel tools for scientists to manage, analyze, segment, and visualize large image datasets and to then use the results to generate surface and volumetric geometric models. These tools are based largely on the Insight Toolkit (ITK) functions and image processing techniques developed by the center's investigators. The latest software provides an application-specific interface to the underlying ITK functionality while hiding many of the details that hinder easy utility. The center is developing specific applications from collaborations with bioscientists that will server as prototypes for the larger biomedical image processing and analysis community.

Simulation tools: Current software supports general scientific computing techniques, such as finite element, finite difference, and boundary element techniques for the numeric solution of bioelectric field problems. The center has also developed novel techniques for regularization techniques to constrain the effects produced by the ill-posed nature of electrocardiogram and electroencephalogram inverse problems. Recently developed simulation tools predict electrical changes in the heart due to ischemia. A current focus is developing interfaces between our integrated software environment and programs created by collaborators; the goal is to minimize the overhead of integrating existing software systems.

Visualization tools: The center builds strongly on the outstanding visualization capabilities of the Scientific Computing and Imaging Institute and seeks to make the most advanced visualization algorithms easily available to biomedical researchers. Specific techniques that the center has implemented include interactive scalar field display, isocontour and isosurface extraction, volume and surface rendering, and vector and tensor field visualization. Current initiatives include quantitative spatio-temporal visualization and methods for the characterization, representation, and presentation of error and uncertainty due to modeling, simulation, and visualization.

Special Features

The center has a specific pathway for adding new collaborations and managing them to a successful completion and transition to independent funding. This "collaboration life cycle" seeks to identify collaborative opportunities and provides a means to work with them to generate computational support and tools in a way that also benefits other scientists in related fields. Thus, each collaboration becomes a representative of a broader class of investigators who might benefit from improved computational support. The goal of most collaborations is independent funding that provides the necessary support for ongoing center involvement.

Available Resources

All software developed by the center is open source and in the public domain and is available for download from the center's Web site. Users or potential users with specific needs can thus alter the programs to suit their needs. Moreover, they may approach the center and apply to become supported collaborators and enter the collaboration life cycle. In this case, the center will work directly with the collaborators to develop improved computational tools for their needs and those of other scientists in the same or related fields.

Training Opportunities and Workshops

Training opportunities exist within the center on several levels. Collaborators with whom the center is developing new computational algorithms or tools will receive training in those tools. Many collaborators elect to send members of their teams to spend dedicated time at the center and thus are provided more in-depth training in the use of the software and the opportunity to participate in its further development. The center also conducts annual workshops that are open to all interested parties. The goals of these workshops change slightly from year to year, but they include technical training as well as instruction in the core technical areas that the center supports. Most important, the center uses the workshops to solicit feedback and suggestions for new capabilities.

Publications

Peruse the many publications from the CIBC and the Scientific Computing and Imaging Institute that are related to CIBC's biomedical computing research.