Integrated Software Infrastructure for Image Based Modeling
A persistent challenge to investigators wishing to enter the large domain is the investment in elements of the algorithms and software that lie outside their competence or interest. They may have specialized knowledge in one of the many steps required to solve a multiscale biological problem and wish to focus their research on that domain. However, before even starting, they must create a substantial sequence of software tools, often in areas for which there are few open source solutions available. To meet this need, we have developed and deploy a complete suite of software tools for image based modeling and simulation. The tools are modular, often separate applications that pass data via files, and some elements are integrated tightly into a problem solving environment. They cover all the steps from image visualization through segmentation, registration, mesh generation, application of boundary conditions, numerical solutions to a range of problems in bioelectricity, and comparison of computed and measured results. The entire pipeline is supported but a parallel suite of visualization tools that seek to manage large data sets efficiently with emphasis on interactive modes of visualization. Support for the software development comes from sophisticated software engineering tools and practices, including element and integrated testing, bug tracking, and online documentation. The entire suite is freely available using industry standard open source management and release tools via Github. We continue to expand both the native capabilities of the software and also to leverage progress from other partners including such projects as TetGen, 3DSlicer, and CARP. We also support open source collaborative projects through related data repositories and leadership in the ECG Imaging Consortium and Computing in Cardiology. Finally, for the past 4 years we have conducted a two-week summer course to instruct participants in the entire image based modeling pipeline. In this presentation I will summarize our system, recent progress, and open opportunities for additional collaborations.