Geometric Modeling

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Biomedical Computing Collaboration Challenges
Chris Johnson Scientific Computing and Imaging
Institute University of Utah www.sci.utah.edu
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Biomedical Imaging and Modeling
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Biomedical Simulation
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Biomedical Visualization
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A Biology/Bioengineering Grand Challenge
Modeling, Simulation, Visualization, Software
Frameworks, Databases, Networking, Grids
Courtesy Peter Hunter, University of Auckland
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Bioengineering Example
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Software SCIRun, BioPSE, PowerApps

• Computational Workbench
• Image Processing, Modeling, Simulation,
  Visualization Tools
• Layered Software System
• Dataflow/Modules
• PowerApps
• Interactive Problem Set up and Computing
• What if..? Problem Exploration
• Flexible, Extensible Environment
• Open Source Software (MIT Public License)
• Module Development Tool and Bridging
• PowerApps (BioFEM, BioTensor, BioImage)
• Irix, Linux, Mac OSX, Windows

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SCIRun/BioPSE Extensibility

• Leverage existing utilities/programs
• Extensibility through bridges

VisTrails
Matlab
NetSolve
SQL
lib
socket
BioPSE
PETSc
lib
ITK
lib
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Cardiac Electrical Wave Propagation
Structural and chemical information
Cellular model of electrical conductivity/ action
potential propagation
Bidomain model of an ischemic heart
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Software Tool Integration
Computational Cardiology Software Integration
Example
Matlab for cellular modeling and some numerics
Matlab tools
CardioWave is specially designed to run on a
cluster to compute bidomain simulations
CardioWave Simulation tool
SCIRun visualization
SCIRun for visualization, imaging, integration
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SCIRun
gt Data flow paradigm gt Integrating
different programs together gt Advanced
visualization
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HealthGrid, BIRN, Lariat, NCBCs, INBRE
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Guiding Principles

• Driven By Needs of Users
• Accessibility and Usability
• Integration and Extensibility
• Performance and Control
• Software Engineering
• Open Source Open Data Open Science
• Verification and Validation

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Software Engineering
Software Engineering is Often Overlooked! Software
Engineering is Hard! Software Engineering is
Important!
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The Gap
Biomedical Sciences
CS, Math, CSE
Biomedical Computing
Biomedical Sciences
CS, Math, CSE
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Information Big Bang
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NIH/NSF Visualization Research Challenges Report
http//tab.computer.org/vgtc
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PITAC Reports www.nitrd.gov
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More Information

• www.sci.utah.edu
• crj_at_sci.utah.edu

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IEEE Computer Graphics and Applications,
July/August, 2004 www.sci.utah.edu
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Top Visualization Research Issues

• Think About the Science
• Quantify Effectiveness
• Error and Uncertainty Visual Representation
• Perceptual Issues
• Novel Hardware Architectures
• HCI
• Global/Local Visualization
• Time Dependent Visualization
• Integrated PSEs
• Multi-field Visualization
• Integrating Info and Sci Visualization
• Interesting Feature Detection
• Scalable, Distributed and Grid-Base Visualization
• Theory of Visualization

IEEE Computer Graphics and Applications,
July/August 2004
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Grid Visualization Algorithms

• Compression (wavelets, multiresolution, mpeg,
  etc.)
• Importance Based Rendering
• View Dependent
• Image Based Rendering
• Adaptive (Resource Aware) Parallel/Distributed
  Techniques

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Volume Rendering
Maximum Intensity Projection (MIP)
Full Volume Rendering
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Volume Rendering
enamel / background
dentin / pulp
dentin / background
dentin / enamel
1D not possible 2D specificity not as good
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Visualization Software BioImage
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Time Dependent Visualization
Time-dependent BioImage volume rendering of a 4D
CT dataset. Interaction rate on a PC running
Linux is approximately 10 frames per second.
Data from collaborator George Chen (MGH).
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VisTrails History Management
A single VisTrail is a complete collection of
dataflows!
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VisTrails Multi-View Functionality
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ITK An Interactive Segmentation Tool
www.itk.org
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Large-Scale Images
Images courtesy of Mark Ellisman, UCSD
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Large-Scale Imaging/Visualization
Image courtesy of Art Toga, UCLA
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New Visualization Techniques
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Visualization Algorithm Scalability
Speedup for k n0.8
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NOISE
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Speedup
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Visible Woman CT Dataset 1Gb MC - 280s
4.5m PISA - .17s Mac G5, 2Ghz
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107
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1010
1011
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Volume Size