NCRR Overview Center for Bioelectric Field Modeling, Simulation and Visualization Chris Johnson (PI) Rob MacLeod (Co-PI) Chuck Hansen (Co-PI) University of Utah

NCRR Overview Schedule Monday July :30-9:00Breakfast 60 9:00-10:00Center Highlights, Brief Overview and Response to 2002 EAB Report :00-12:00BioPSE and map3d Demos 90 12:00-1:30Lunch and Executive Session 30 1:30-2:00Software Engineering and Release/Documentation 60 2:00-3:00BioPSE 90 3:00-4:30Research Progress 60 4:30-5:30EAB Executive Session 6:30Dinner Tuesday July :30 - 9:00 Breakfast 30 9:00 - 9:30Education and Dissemination 90 9: :00Hands-on Demos 60 11: :00Future Directions 60 12:00 - 1:00Discussion with Center Admin 1:00Optional Lunch Research Demos - Head/Torso large-scale forward simulation: (Dave Weinstein) - Mouse ECG – Collaboration with Duke University (Dave Weinstein) - Nerve fiber modeling: (Chris Butson) - EIT: Determination of electrical conductivities (Chris Johnson) - BEM: Cardiac forward problem (Rob MacLeod) -map3d (Rob MacLeod) - Image Toolkit (ITK): Segmentation of head/brain with tumor (Darby Van Uitert)

NCRR Overview Center Time Line Started - September 15, 1999 Fully Staffed - May, st Code Release – February, st EAB Meeting – April, BioPSE Downloads – Feb, th Code Release – March, nd EAB Meeting – March, 2002 Renewal Site Visit – March, rd EAB Meeting – July th EAB Meeting – Spring th EAB Meeting – March 2005 Renewal Site Visit – March 2005

NCRR Overview Aims and Objectives Develop and Implement : An integrated, extensible, problem-solving environment (BioPSE) Bioelectric field simulation research and tools Geometric modeling research tools Visualization resaerch and tools

NCRR Overview Responses to EAB Recommendations EAB: The Center has been very good at adapting to change – in particular the recognition of the need to move their software to Linux PCs with the fast graphics cards now available. The EAB strongly supports continuing efforts to make the software robust across platforms and operating system versions. Center: The Center has continued its support of Linux and expanded support to additional graphics cards. In addition, we have recently created a Mac OSX version of SCIRun and BioPSE.

NCRR Overview Responses to EAB Recommendations EAB: Whenever practicable, the Center should make use of guidance and (open source) software from other research labs. It is important that the Institute developers be aware of similar developments going on in other labs. For example, the MRI geometric distortion and field bias correction might benefit from a close connection to developments in other laboratories. Center: We have expanded our use of open source software engineering tools, and continue to look for better, available tools. Over this past year, we undertook a major effort to port the NIH’s Image Toolkit (ITK) to SCIRun/BioPSE. You will see demonstrations of the BioPSE/ITK integration. We have also integrated other open source software packages (PETSc, Teem, gtk) within BioPSE and map3d.

NCRR Overview Responses to EAB Recommendations EAB: The success of the Center depends on achieving a working relationship with other development centers as well as biomedical scientists and clinicians, and working with these groups will help propagate the use of the software. An area of opportunity for BioPSE is the development of techniques and applications that capitalize on the capability to model realistic anatomy and conductivity tensors. Center: We have new research results on characterizing conductivity tensors. - M. Lazar, D.M. Weinstein, J.S. Tsuruda, K.M. Hasan, K. Arfanakis, E. Meyer, B. Badie, H.A. Rowley, V. Haughton, A. Field, A.L. Alexander. “White Matter Tractography Using Diffusion Tensor Deflection,” In Human Brain Mapping, Vol. 18, pp D.M. Weinstein, L. Zhukov. “Diffusion Tensor MRI Visualization: from Acquisition to Application,” IEEE Visualization, 2003 (Workshop). We have worked with collaborators at Northeastern, RPI, and U. of Oregon to create a new EIT BioPSE network. We’ve collaborated with Duke Univ. on a new mouse heart/torso model. You will see an EIT and Mouse ECG demos today.

NCRR Overview Responses to EAB Recommendations EAB: We recognize that one level of user includes bioengineers and others who do appreciate the technical aspects of the user interfaces, but we strongly encourage the development of pre-packaged applications for biologists which only present biologically relevant information, but still allow the interested user to delve down into control structures and code. Map3d appears more user-driven and this has been under development for longer and BioPSE should move in the same direction. Center: We are currently developing several pre-packaged BioPSE-based applications, including BioPSE-Vis, BioPSE- Image, BioPSE-Model, BioPSE-Sim. We will present overviews of our ideas for new pre-packaged applications.

NCRR Overview Responses to EAB Recommendations EAB: Therefore the group will need to develop more dynamic documentation techniques including the development of web-based/living documents, technical writing expertise and other means to keep up with anticipated fast-paced developments. Center: We have greatly expanded our web-based/living documents. As a matter of fact, our documentation is now published hourly. In addition, we have added documentation for BioPSE networks. During the “hands- on” portion of the EAB Meeting, the EAB members will have a chance to interact and use the documentation directly.

NCRR Overview Responses to EAB Recommendations EAB: There are clearly very good links with the cardiac community but the EAB feels that the group needs to develop stronger connections with the neural community. Center: We have greatly increased both our connections with the neural community (by new research collaborations) and by having a stronger presence at neuro-related conferences and publications (Human Brain Mapping, Society of Neuroscience 2003, Neuroinformatics 2003, NFSI). We plan to continue to increase our neuro-based Center activities.

NCRR Overview Responses to EAB Recommendations EAB: One strategy for gaining wide spread acceptance of BioPSE may be to develop educational components for the software, for example, using the software to train medical students in cardiac electrophysiology. Center: This past year, we started experimenting with BioPSE as an educational software tool. During the “hands-on” portion of the meeting, the EAB members will have a chance to see and try out some of the BioPSE networks created for a Bioengineering course. In addition, the handouts to the course are in your folders.

NCRR Overview Responses to EAB Recommendations EAB: The development efforts should continue to focus on the existing scientific base in the cardiac and neurophysiology, but these efforts could very well expand into other application areas in the future, as driven by the biomedical user community. Center: We absolutely agree! We plan to make this a major topic of discussion during this EAB meeting and seek further guidance from the EAB.

NCRR Overview Research Highlights Accomplishments: Inverse MEG Simulation Inverse AMG BioPSE/ITK Integration Neural Stimulation Model New Constrained Inverse Technique Simulating Myocardial Ischemia Mouse Heart Simulation Building block: hexagon Building block: hexagon Cluster of 27 myocytes Capillaries

NCRR Overview BioPSE Highlights Over 20 new BioPSE modules created! User manual, developer’s manual, and tutorial

NCRR Overview Software Releases BioPSE Version June, 2003 Open Source Target platforms: –Linux, Irix, Mac OSX –Single and multiprocessors map3d Version 5.4 March, 2003 Target platforms: – Linux, Windows, Irix, (Mac OSX)

NCRR Overview BioPSE Web Statistics SCIRun downloads since Jan 2003: 807 BioPSE downloads since Jan 2003: 256 SCIRun downloads since initial release: 3500 BioPSE downloads since initial release: 1200 Successful hits for software.sci.utah.edu since Jan 2003: 633,441 Visits For software.sci.utah.edu since Jan 2003: 49,037 Successful Hits For since Jan 2003: 1,940,795www.sci.utah.edu Visits For since Jan 2003: 162,158www.sci.utah.edu Average time for visit: 5 minutes 20% of visitors visited more than once From 2002 to 2003, we have doubled the number of visitors to the software site.

NCRR Overview Center Organization Chart External Advisory Board Technical Manager ( D. Weinstein) Collaborators Directors (C. Johnson and R. MacLeod) Modeling Research (R. MacLeod, Ph.D.) Visualization Research (C. Hansen. Ph.D.) Simulation Research (C. Johnson, Ph.D.) PSE Research (S. Parker, Ph.D.) Software Engineering D. De St. Germain Administrator (A. Betancourt) Media Specialist (R. Coffey) Systems (R. Cummins) Associate Director ( G. Jones, Ph.D. )

NCRR Overview Center Personnel Chris Johnson Rob MacLeod Chuck Hansen Steve Parker Dana Brooks Dave Weinstein* Allyne Betancourt Ted Dustman McKay Davis Marty Cole Open Postdoc Mike Callahan Darby Van Uitert Brandon Mansfield Bryan Worthen Chris Butson Gordon Kindlmann Sasch Moehrs ** Andrew Shafer ** Alexei Samsonov Laura Traynor * Robert Van Uitert Kris Zyp * Yesim Serinagaoglu Alireza Ghodrati * Graduated** New

NCRR Overview Collaborator Overview 3D Cardiac Mapping Taccardi Cortical Mapping McCarley Neurosurgery Modeling and Visualization Kikinis Inverse ECG Rudy Cardiac Propagation Henriquez Cardiac Simulation Leon Model SimVis Core BioPSE Inverse EEG Makeig EEG/MEG Nenonen Electromechanics McCulloch

NCRR Overview Service, Training, and Dissemination Disseminate or Provide: State-of-the-art software and documentation developed within the Center –New software releases and large documentation effort An on-line database of geometric models and simulation data –New torso and head models on-line Short courses on the use of Center software tools –BioPSE short course held August, 2002 Workshops on bioelectric field research –Minisymposium on Computational Bioelectric Fields – SIAM 50 th Anniversary Conference –Scientific Visualization with SCIRun, SIAM CSE 2003 –Integrating Visualization with Modeling and Simulation for Biomedical Applications. IEEE Visualization 2003

NCRR Overview

NCRR Overview Leadership 9 Journal Editorial Boards 12 Advisory Boards (5 NCRRs) 10 Chair: National Conferences and Workshops 20+ Keynote or Plenary Presentations (more scheduled) 50+ Conference Program or Organizing Committees 50+ Peer Reviewed Papers and Book Chapters

NCRR Overview Awards Chris Johnson was promoted to the rank of Distinguished Professor, the youngest to achieve the rank in University of Utah history. Steve Parker received the Computerworld Honors Medal of Achievement. The award is presented annually to men and women around the world who have made outstanding progress for society through the visionary use of information technology.

NCRR Overview Visualization Excellence IEEE Visualization 2002 Best Paper Award IEEE Visualization 2001 Best Paper Award IEEE Visualization 2001 Best Panel Award IEEE Visualization 2000 Best Panel Award IEEE Visualization `99 Best Paper Award IEEE Visualization `98 Best Paper Award ACM Volume Visualization `98 Best Paper Award IEEE Visualization `97 Best Panel Award

NCRR Overview More Information

NCRR Overview Schedule Monday July :30-9:00Breakfast 60 9:00-10:00Center Highlights, Brief Overview and Response to 2002 EAB Report :00-12:00BioPSE and map3d Demos 90 12:00-1:30Lunch and Executive Session 30 1:30-2:00Software Engineering and Release/Documentation 60 2:00-3:00BioPSE 90 3:00-4:30Research Progress 60 4:30-5:30EAB Executive Session 6:30Dinner Tuesday July :30 - 9:00 Breakfast 30 9:00 - 9:30Education and Dissemination 90 9: :00Hands-on Demos 60 11: :00Future Directions 60 12:00 - 1:00Discussion with Center Admin 1:00Optional Lunch Research Demos - Head/Torso large-scale forward simulation: (Dave Weinstein) - Mouse ECG – Collaboration with Duke University (Dave Weinstein) - Nerve fiber modeling: (Chris Butson) - EIT: Determination of electrical conductivities (Chris Johnson) - BEM: Cardiac forward problem (Rob MacLeod) -map3d (Rob MacLeod) - Image Toolkit (ITK): Segmentation of head/brain with tumor (Darby Van Uitert)