Transcript National Alliance for Medical Image Computing: Namic

NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
Slicer Progress
in 2009
Steve Pieper, Ph.D.
Topics
• 2009 Year in Review
• Highlights
– Funding Milestones
– New Functionality Examples
• Plans for This Week and Beyond
National Alliance for Medical Image Computing
http://na-mic.org
Slicer Background
• 3D Slicer Role in NA-MIC
– Translation Platform to get Medical Computing
Technology to DBP Researchers
– Provide Reference Implementation using NAMIC Kit
– Part of NA-MIC Outreach to New Applications
• First Slicer3 svn commit: January 26,
2006
National Alliance for Medical Image Computing
http://na-mic.org
Progress in 2009
•
• Numbers 2009
– Subversion Commits: 3,224 (11,541
total)
– Lines of Code*: 914,466
– Bugs & Features:
• 336 Submitted
• 156 Closed
– Active Developers†: 68
Numbers 2007
– Subversion Commits: 3,407
– Lines of Code*: 371,428
– Bugs & Features:
• 154 Submitted
• 63 Closed
– Active Developers†: 33
• 3D Slicer Version 3.4/3.4.1
– Released May/October, 2009
*: find . -iname \*.h -o -iname \*.cxx -o -iname \*.tcl -o -iname \*.java -o -name \*.py | grep -v svn | xargs wc
(does not include libraries or modules in external repositories)
†: svn log | grep "^r" | cut -d " " -f 3 | sort | uniq | wc
National Alliance for Medical Image Computing
http://na-mic.org
Funding Milestones of 2009
• Slicer has Key Role in National Center for Image
Guided Therapy (NCIGT – Jolesz, BWH)
– Renewed for 5 years
• ARRA Supplements
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Annotations (Pohl, IBM)
EMSegmenter (Pohl, IBM)
Registration (Meier, BWH)
Workflow (Zeitzev, BWH)
Qt (Finet, Fillion-Robin, Kitware)
Slicer Quality (Wallace, MGH)
• NA-MIC Renewal (shipped)
• Harvard Catalyst (CTSA), R01 Collaborations…
National Alliance for Medical Image Computing
http://na-mic.org
Extension Modules
• Allow Distribution
of Plug-in
Functionality
• 27 Extensions
From NA-MIC
Developers,
Investigators and
Collaborators
• Command Line,
Scripted,
Loadable…
National Alliance for Medical Image Computing
http://na-mic.org
ABC.s3ext
ARCTIC.s3ext
BRAINSDemonsWarp.s3ext
BRAINSFit.s3ext
BRAINSMush.s3ext
BRAINSROIAuto.s3ext
EMFiberClusteringModule.s3ext
ExampleCommandLine.s3ext
ExampleLoadableGuiLessModule.s3ext
ExampleLoadableModule.s3ext
FourDAnalysis.s3ext
FuzzySegmentationModule.s3ext
HammerRegistration.s3ext
LabelDiameterEstimation.s3ext
LesionSegmentationApplications.s3ext
LupusLesion.s3ext
PythonSampleScriptedModule.s3ext
SkullStripperModule.s3ext
TclSampleScriptedModule.s3ext
VMTKCenterlines.s3ext
VMTKEasyLevelSetSegmentation.s3ext
VMTKLevelSetSegmentation.s3ext
VMTKVesselEnhancement.s3ext
VmtkSlicerModule.s3ext
examples.s3ext
plastimatch-slicer.s3ext
robustStatisticsSeg.s3ext
Longitudinal Imaging
• Volume Compare View
Mode (Miller, GE)
– Shown with 5 MRI MS
Lesion Time Points
(Guttmann, Meier, BWH)
• FourDVolume Module
(Takuda)
– MR Perfusion Time Series
National Alliance for Medical Image Computing
http://na-mic.org
Improved Infrastructure
• Extract Subvolume
ROI (Fedorov, BWH)
• Dual 3D Camera
View (Barre, Kitware)
• Hardware
Accelerated Volume
Rendering (Lui, Lisle,
NCI, Kviz)
National Alliance for Medical Image Computing
http://na-mic.org
PET CT Module
• Standardized Uptake
Value (SUV) Computation
(Plesniak, BWH)
– Important for Clinical
Translational Research
(Complete Open Source
PET Solution)
– Demonstrated at RSNA
2009
– More Information in
Training Session
National Alliance for Medical Image Computing
http://na-mic.org
White Matter Anatomy
• Exploration of White
Matter Structures in
Language
Processing
(Lemaire, Golby)
– Use Structural, DTI,
fMRI
National Alliance for Medical Image Computing
http://na-mic.org
Neurosurgery Tractography
• Surgical Plans based on
Structural, DTI, and fMRI
Displayed in OR (Golby,
Norton, O’Donnell BWH)
• Tracked Surgical Instruments
Control Seed Points for
Tractography (Golby, Liu,
Hata, Papdemetris, BWH,
Yale)
– OpenIGTLink to BrainLab
Navigation System
National Alliance for Medical Image Computing
http://na-mic.org
Major Projects for 2010
• Major Rewrite of Slicer GUI to use Qt to
Replace KWWidgets
– Enabled by License change when Nokia
Purchased Qt
– Slicer Architecture Enables Smooth Transition
for MRML, Command Line Modules
– Slicer 3.5 Supports Both Qt and KWWidgets in
Common Runtime Process
• KWWidgets Modules will be Supported Through
2010 and into 2011 During Qt Port
National Alliance for Medical Image Computing
http://na-mic.org
More Work for 2010
• Increased Emphasis on TESTING
• Increased Use of Extension Modules
• Emphasis on Python as Scripting,
Numeric, and Parallelization Tasks
National Alliance for Medical Image Computing
http://na-mic.org