Utah NCRR Advisory Board Meeting 2004
Overview
NCRR
Schedule
Overview
Thursday August 5
Research Demonstrations
8:15 - 8:45 Breakfast at SCI Institute
Heart
- map3d: visualization of mouse timedependent mouse ECG data
8:45 - 9:45 Center Highlights, Overview and
Response to 2003 EAB Report
9:45 - 10:00 Break
10:00 - 11:30 Project Summaries I
11:30 - 12:30 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
- 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
Center Time Line
Started - September 15, 1999
Fully Staffed - May, 2000
1st Code Release – February, 2001
1st EAB Meeting – April, 2001
432 BioPSE Downloads – Feb, 2002
4th Code Release – March, 2002
2nd EAB Meeting – March, 2002
Renewal Site Visit – March, 2002
3rd EAB Meeting – July 2003
4th EAB Meeting – August 2004
Renewal Due - February 1, 2005
5th EAB Meeting - Spring 2005
Renewal Site Visit – Spring 2005
Overview
NCRR
Aims and Objectives
Develop and Implement :
Overview
• An integrated, extensible,
problem-solving environment
(BioPSE)
• Bioelectric field simulation
research and tools
• Geometric modeling research
tools
• Visualization resaerch and tools
NCRR
Responses to EAB Recommendations
Overview
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
User Information - Bioelectric Related
Overview
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
User Information - DTI
Overview
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
User Information - Other
Testing the software. I might use it for a course on FEM Overview
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
Responses to EAB Recommendations
Overview
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
Responses to EAB Recommendations
Overview
EAB: The EAB endorses the Center’s 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 EAB’s 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
Research Highlights
Accomplishments:
• Inverse MEG
Simulation
• Inverse AMG
• BioPSE/ITK Integration
• Neural Stimulation
Model
• New Constrained
Inverse Technique
• Simulating Myocardial
Ischemia
• Mouse Heart
Simulation
Overview
Building block:
hexagon
Capillaries
Cluster of 27 myocytes
NCRR
BioPSE Highlights
Overview
New PowerApps - BioFEM and BioTensor
Major releases Oct 2003 and July 2004
BioImage PowerApp soon (next release)
NCRR
Software Releases
BioPSE
Overview
• Version 1.22.0 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
BioPSE Web Statistics
Overview
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/BioPSE email
list: 538, map3d email list: 318
Successful Hits For www.sci.utah.edu since Jan 2004:
2,675,797 (1,940,7950)
NCRR
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 - 105
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
Overview
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
Center Organization Chart
Overview
Associate
Director
Directors
External Advisory Board
(C. Johnson and
R. MacLeod)
(G. Jones, Ph.D. )
Administrator
(R. Potts)
Collaborators
Technical Manager
( D. Weinstein, Ph.D.)
Media
Specialist
(N. Galli)
Systems
(R. Coffey)
Modeling
Research
Visualization
Research
Simulation
Research
PSE
Research
Software
Engineering
(R. MacLeod, Ph.D.)
(C. Hansen. Ph.D.)
(C. Johnson, Ph.D.)
(S. Parker, Ph.D.)
(D. De St. Germain)
NCRR
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
Overview
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
Graduating Ph.D. Students
Overview
Chris Butson (BE)
Bruce Hopenfeld (BE)
Gordon Kindlmann (CS)
Alexei Samsonov (Physics)
Yesim Serinagaoglu (ECE)
Robert Van Uitert (CS)
NCRR
Collaborator Overview (Old)
Overview
3D Cardiac Mapping
Taccardi
Model
Inverse ECG
Rudy
Cardiac
Propagation
Henriquez
Inverse EEG
Makeig
EEG/MEG
Nenonen
Sim
Cardiac Simulation
Leon
Core
Vis
BioPSE
Electromechanics
McCulloch
Cortical
Mapping
McCarley
Neurosurgery
Modeling and
Visualization
Kikinis
NCRR
Collaborator Overview (New)
Overview
3D Cardiac Mapping
Taccardi
Inverse EEG
Makeig/Worrel
Model
Cardiac
Propagation
Henriquez
Cardiac
Imaging
McVeigh
Sim
Electromechanics
McCulloch
Cortical Variance
Visualization
Toga
Core
Source
Localization
Warfield
Vis
BioPSE
Tumor
Visualization
Chen
Neurosurgery
Visualization
Kikinis
DTI Visualization
Hsu
Image-based
Phenotyping
Keller
DWI
Tuch
NCRR
Service, Training, and Dissemination
Disseminate or Provide:
Overview
• 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
Leadership (2000 - 2004)
Overview
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
Impact
6th Annual Symposium on Computer Overview
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
Future and Strategic Planning
Overview
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
Proposed New Center Model
Overview
ITK,
Slicer,
etc.
Imaging and Analysis
VTK,
IDL,
etc.
Visualization
Cubit,
Tetra,
etc.
Modeling
Simulation
Cardio
Wave,
EEGLab,
Brainstom
,
NeuroFEM
etc.
BioPSE
CCA,Loni,etc
NCRR
Center Evolution
Overview
NCRR
Center Roadmap
Overview
NCRR
More Information
Overview
www.sci.utah.edu/ncrr
crj@sci.utah.edu
macleod@cvrti.utah.edu
hansen@cs.utah.edu
dmw@sci.utah.edu
NCRR
Schedule
Overview
Thursday August 5
Research Demonstrations
8:15 - 8:45 Breakfast at SCI Institute
Heart
- map3d: visualization of mouse timedependent mouse ECG data
8:45 - 9:45 Center Highlights, Overview and
Response to 2003 EAB Report
9:45 - 10:00 Break
10:00 - 11:30 Project Summaries I
11:30 - 12:30 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
- 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