The Center for Integrative Biomedical Computing (CIBC)
The Center for Integrative Biomedical Computing is dedicated to producing opensource software tools for biomedical image-based modeling, biomedical simulation and estimation, and the visualization of biomedical data. The Center works closely with software users and collaborators in a range of scientific domains to produce user-optimized tools and provides advice, technical support, workshops, and education to enhance user success. Biological projects and collaborations drive our development efforts, all with a single unifying vision: to develop the role of image-based modeling, simulation, and visualization in biomedical science and clinical practice."The success of computational biology is shown by the fact that computation has become integral and critical to modern biomedical research. Because computation is integral to biomedical research, its deficiencies have become significant rate limiting factors in the rate of progress of biomedical research."
From Eric Jakobsson, the NIH Roadmap on Computing, 2004
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.