History of the Center for Integrative Biomedical Computing


CIBC Timeline showing the introduction of software, new releases, workshops, and publication counts.

The CIBC originally began as the NIH Center for Bioelectric Field Modeling, Simulation, and Visualization on September 15, 1999. During the first five years, the Center focused on creating an extensible, scalable, scientific problem-solving environment (PSE) and on developing corresponding research to solve real-world problems relating to bioelectric fields. To accomplish this goal, we conducted research and development in advanced modeling, simulation, and visualization methods for solving bioelectric field problems; we also created BioPSE, an extension to the existing SCIRun, which is a modular, extensible, integrated soft-ware problem-solving environment for bioelectric field problems. The SCIRun software supported interaction among the modeling, computation, and visualization phases of bioelectric field simulation with BioPSE providing specific extensions for the Center.

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Screenshots from the original version of SCIRun demonstrating bioelectric field modeling.

In 2005, following the NCRR renewal, the Center was renamed the Center for Integrative Biomedical Computing (CIBC). At this time, the Center reengineered SCIRun to separate the underlying filters or modules from the dataflow interface. The Center also began integrating third-party packages into its tools, such as the Insight Toolkit (ITK), in turn assisting in the latest generation of Center applications, such as map3d, ImageVis3D, Seg3D, BioMesh3D, and ShapeWorks.

Another example of a highly successful application from the Center is Seg3D, which performs user-guided image processing and segmentation. Seg3D is also based on the Insight Toolkit and presents through a simple user interface the appropriate filters and segmentation algorithms with some settings pre-selected based on our experience with data sets from our collaborators. By providing interactive access to the relevant parameters with experience-based guidelines and constraints imposed, Seg3D seeks to make available to biomedical users a powerful set of capabilities in a form that is inviting and easy yet efficient to use.

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Original version of Seg3D being used to segment and view structures from a CT scan.

Now, the Center's tools assist researchers' investigations in such areas as cardiac electro-mechanical simulation, ECG and EEG forward and inverse calculations, modeling of deep brain stimulation, EMG calculation, determination of the electrical conductivity of anisotropic heart tissue, orthopedics, and a number of other areas. The Center has made significant advances in the area of bioelectric field simulation, modeling, and visualization. We created new approaches to the solution of forward and inverse problems in both cardiology and neurology, using SCIRun to both carry out the research and as a repository for its products. We developed several new methods for the visualization of three-dimensional data sets and translated award-wining, cutting-edge visualization research into working capabilities in SCIRun, map3D, Seg3D, and ImageVis3D. Because we believe that the ability of researchers to compare their new ideas, techniques, and data with those of other researchers is crucial to scientific process, we have gathered high-quality data sets and made them freely available to the scientific community. We have also released a set of images and associated geometric models, from which we have computed simulations and prepared visualizations. The Center has made every aspect of our research available to other researchers for validation and comparison of their own methods. We believe providing such resources will accelerate progress in biomedical computing and biomedical science in general.

The most important measure of the Center's success has been the number of scientists using the resources we provide. Since our renewal in 2005, there have been over 11,000 downloads of SCIRun, more than 8000 downloads of BioPSE (all from outside the Center and our affiliate institutions), over 7000 downloads of BioImage and Seg3D, and almost 4000 downloads of the CIBC data sets. Since December 2008, there have already been more than 2000 downloads of ImageVis3D. Since the year 2000, over 200 papers published by scientists outside the Center have included at least one reference to CIBC software or the underlying SCIRun infrastructure. During the same time, members of the Center have been listed among the authors of over 175 publications related to biomedical computing in a wide range of technical and biomedical journals and conference proceedings.

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