NCRR Overview Utah NCRR Advisory Board Meeting 2004 NCRR Overview Schedule Thursday August 5 8:15 - 8:45 Breakfast at SCI Institute 8:45 - 9:45 Center Highlights, Overview and Response to 2003 EAB Report 9: :00 Break 10: :30 Project Summaries I 11: :30 Lunch and Executive Session 12:30 - 2:00 Project Summaries II (VSC) 2:00 - 2:15 Break 2:15 - 3:45 Future Directions 3:45 - 4:45 EAB Executive Session 4:45 - 5:45 Discussion with Center Administration 6:00 p.m. Drive to Hotel/Dinner 6:30 Dinner at Bambara, Hotel Monaco Research Demonstrations Heart - map3d: visualization of mouse time- dependent mouse ECG data - BioPSE: demonstration of new dataflow and infrastructure features (data import / export, MATLAB, data bundles, module creation, subnets, annotation) Brain - BioPSE: multi-field visualization of scalar and tensor cortical variance data Tumor - BioPSE: new Volume Rendering functionality (tooth dataset) - Dynamic PowerApp: new PowerApp for image processing (mouse dataset) Tissue Characterization - BioTensor: demonstrate neural diffusion tensor MRI processing and visualization PowerApp 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 August 2004 Renewal Due - February 1, th EAB Meeting - Spring 2005 Renewal Site Visit Spring 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: Better tracking of the user community and active follow-up. Currently tracks web accesses and downloads but does not gather any information from the users about their intended use of the software and models. The Board recommends that the Center gather some information from uses when they download the site. This will help quantify the impact of the resource. Tracking should include user research areas and any active grants. Center: Since the last EAB Meeting, the Center has started to gather additional information from users and better track research areas (see next slides for examples). NCRR Overview User Information - Bioelectric Related Simulate the electric and magnetic field generated by the heart. Heart electro-mechanical simulation in application to EGM surface and ECG calculation problems Electric field simulation Work in PhD Degree related to Cardiac activation Cardiac electrophysiology To study the conductivity difference in the left ventricle while ischemia occurs Electromechanical mapping of the heart Head model comparison in the case of epilepsy data Determination of the electrical conductivity of anisotropic heart tissue. NCRR Overview User Information - DTI DTI in malignant brain lesions Biomedical image analysis and visualization Diffusion Tensor Imaging and Functional Connectivity Exploration of diffusion tensor issues Tools in fMRI, especially tensor field visualization Fiber tracking View DTI dataset Visualizing MRI/CT/PET microscopic imagery Visualize diffusion tensor data Calculate diffusion tensor data in several neurologic diseases Brain DTI Tractography DTI in MS patients Diffusion tensor research and software development NCRR Overview User Information - Other Testing the software. I might use it for a course on FEM HIV/aging Analyzing EMF health effects provoked by underground and overhead transmission lines Computer aided surgery 3D data visualization of numerical simulations Work in subsurface sensing and imaging Teaching of physiology and pharmacology We do work in biological modeling and virtual reality Three dimensional structure of macromolecules MRI Views for breast tumor brachytherapy Investigation of using SCI software to simulate NDT Investigation of civil infrastructure Dental modeling For an NIH proposal NCRR Overview Responses to EAB Recommendations EAB: Actively pursue and engage collaborations that push the package into useful new directions. Biology driven developments should have priority. New areas may also include high performance platforms and grid based computing. These collaborations should capitalize on the visualization, modeling and simulation strengths of the group. Center: The Center has actively pursued and engaged in new collaborations that are both driven by biological problems, as well as leveraging our technological strengths. Examples are new collaborations in: brain imaging and visualization, mouse heart simulation, bioelectric tissue classification, tumor imaging, and several others. NCRR Overview Responses to EAB Recommendations EAB: The EAB endorses the Centers interest in expanding their application domain in ways that compliment the existing base and that leverage the existing computational infrastructure. The listing of topics under Future Directions is the EABs prioritization of possible target domains of future biomedical applications. Center: The EAB listed prioritized future research and development directions as EIT, DTI, Biomagnetic Simulation, and Multiscale Modeling. The Center has responded in expanding its application domain to include these new areas. Specific examples include EIT research with Dana Brooks of Northeastern University, DTI research with Elliot McVeigh at NIH and Art Toga of UCLA and internal research at Utah, Biomagnetic simulation research in brain source localization (Carsten Wolters) and effects of conductivity on brain source localization (Robert Van Uitert), as well as multiscale modeling and simulation efforts with Craig Henriquez at Duke University. 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 New PowerApps - BioFEM and BioTensor Major releases Oct 2003 and July 2004 BioImage PowerApp soon (next release) NCRR Overview Software Releases BioPSE Version July, 2004 Open Source (new MIT public license) Target platforms: Linux, Irix, Mac OSX Windows is under way (via VI) Single and multiprocessors map3d Version 6.1 July, 2004 gtk based Target platforms: Linux, Windows, Irix, Mac OSX NCRR Overview BioPSE Web Statistics SCIRun/BioPSE downloads since Jan 2004: 1114 (1063) SCIRun/BioPSE downloads since initial release: 10,051 map3d downloads since Jan 2004: 342 map3d downloads since release: 1190 Current subscribers to the SCIRun/BioPSElist: 538, map3dlist: 318 Successful Hits Forsince Jan 2004:www.sci.utah.edu 2,675,797 (1,940,7950) NCRR Overview BioPSE Downloads by Country Ascension Island - 1 Argentina - 5 Austria - 10 Australia - 29 Belgium - 9 Bulgaria - 2 Brazil - 25 Belarus - 1 Canada - 38 Cocos Islands - 2 Switzerland - 20 Chile - 3 China - 48 Colombia - 2 Cuba - 2 Christmas Island - 2 Czech Republic - 9 Denmark - 8 Estonia 3 Spain - 30 Ethiopia - 1 Finland - 12 France 52 Germany Greece - 7 Croatia - 2 Hungary - 5 Ireland - 2 Israel - 7 India - 10 Italy - 59 Japan - 31 Korea, Republic of - 16 Lebanon - 1 Lithuania - 2 Latvia - 3 Morocco - 1 Malta - 1 Mauritius - 1 Mexico - 18 Malaysia - 2 Nigeria - 1 The Netherlands - 25 Norway - 8 New Zealand - 2 Philippines - 1 Pakistan - 2 Poland - 26 Portugal - 11 Romania - 17 Russia - 31 Sweden - 10 Singapore - 9 Slovakia - 9 South Africa - 4 Thailand - 2 Turkey - 7 Taiwan - 18 Ukraine - 2 United Kingdom - 62 Uruguay - 2 Venezuela - 1 Vietnam - 2 NCRR Overview Center Organization Chart External Advisory Board Technical Manager ( D. Weinstein, Ph.D.) 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 (R. Potts) Media Specialist (N. Galli) Systems (R. Coffey) Associate Director ( G. Jones, Ph.D. ) NCRR Overview Center Personnel Chris Johnson Rob MacLeod Chuck Hansen Steve Parker Dana Brooks Dave Weinstein Carsten Wolters Raelynn Potts Dav de St. Germain Richard Coffey Erik Jorgensen Nathan Gali Ted Dustman McKay Davis Mike Callahan Darby Van Uitert Bryan Worthen Chris Butson Milan Ikits Bruce Hopenfeld Gordon Kindlmann Andrew Shafer Alexei Samsonov Robert Van Uitert Yesim Serinagaoglu Alireza Ghodrati NCRR Overview Graduating Ph.D. Students Chris Butson (BE) Bruce Hopenfeld (BE) Gordon Kindlmann (CS) Alexei Samsonov (Physics) Yesim Serinagaoglu (ECE) Robert Van Uitert (CS) NCRR Overview Collaborator Overview (Old) 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 Collaborator Overview (New) 3D Cardiac Mapping Taccardi Neurosurgery Visualization Kikinis Cardiac Propagation Henriquez Model SimVis Core BioPSE Inverse EEG Makeig/Worrel Electromechanics McCulloch Source Localization Warfield Cardiac Imaging McVeigh Tumor Visualization Chen Image-based Phenotyping Keller Cortical Variance Visualization Toga DTI Visualization Hsu DWI Tuch 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 data sets on-line (DTI data set, Matlab data sets, and Volume data sets) Short courses on the use of Center software tools BioPSE 3 day course held December 2003 Workshops and Demonstrations on Center software and research Diffusion Tensor Imaging Workshop, IEEE Visualization Conference, Seattle, October 2003 The BioPSE software system, NCRR booth, SuperComputing 2003 BioPSE demonstration, NIH - BISTI Digital Biology, Bethesda, November 2003 Diffusion Tensor Imaging Mini Symposium, Imaging Sciences 2004 NCRR Overview NCRR Overview Leadership ( ) Over 140 peer reviewed publications Multiple major code releases (SCIRun, BioPSE, PowerApps, and map3d) 12+ editorial boards 12 advisory boards (5 NCRRs) 14+ chaired conferences or workshops 50+ conference or program committees Over 40 keynote or plenary talks 350+ visitors at the SCI Institute NCRR Overview Impact 6th Annual Symposium on Computer Methods in Biomechanics and Biomedical Engineering 2004 Best Paper Award Visualization 2003 Best Panel Award Visualization 2002 Best Paper Award Visualization 2001 Best Paper Award Visualization 2000 Best Panel Award Visualization 1999 Best Paper Award Visualization 1998 Best Paper Award Volume Visualization 1998 Best Paper Award Visualization 1997 Best Panel Award NCRR Overview Future and Strategic Planning To better reflect the growth in scope and users of our Center, we would like to discuss: Broadening the mission of our Center Renaming our Center Strategies for our 2005 renewal NCRR Overview Proposed New Center Model Modeling Simulation Visualization Imaging and Analysis BioPSE ITK, Slicer, etc. Cubit, Tetra, etc. VTK, IDL, etc. Cardio Wave, EEGLab, Brainstom, NeuroFEM etc. CCA,Loni,etc NCRR Overview Center Evolution NCRR Overview Center Roadmap NCRR Overview More Information NCRR Overview Schedule Thursday August 5 8:15 - 8:45 Breakfast at SCI Institute 8:45 - 9:45 Center Highlights, Overview and Response to 2003 EAB Report 9: :00 Break 10: :30 Project Summaries I 11: :30 Lunch and Executive Session 12:30 - 2:00 Project Summaries II (VSC) 2:00 - 2:15 Break 2:15 - 3:45 Future Directions 3:45 - 4:45 EAB Executive Session 4:45 - 5:45 Discussion with Center Administration 6:00 p.m. Drive to Hotel/Dinner 6:30 Dinner at Bambara, Hotel Monaco Research Demonstrations Heart - map3d: visualization of mouse time- dependent mouse ECG data - BioPSE: demonstration of new dataflow and infrastructure features (data import / export, MATLAB, data bundles, module creation, subnets, annotation) Brain - BioPSE: multi-field visualization of scalar and tensor cortical variance data Tumor - BioPSE: new Volume Rendering functionality (tooth dataset) - Dynamic PowerApp: new PowerApp for image processing (mouse dataset) Tissue Characterization - BioTensor: demonstrate neural diffusion tensor MRI processing and visualization PowerApp