NA-MIC National Alliance for Medical Image Computing Slicer Progress in 2009 Steve Pieper, Ph.D.

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Presentation transcript:

NA-MIC National Alliance for Medical Image Computing Slicer Progress in 2009 Steve Pieper, Ph.D.

National Alliance for Medical Image Computing Topics 2009 Year in Review Highlights –Funding Milestones –New Functionality Examples Plans for This Week and Beyond

National Alliance for Medical Image Computing Slicer Background 3D Slicer Role in NA-MIC –Translation Platform to get Medical Computing Technology to DBP Researchers –Provide Reference Implementation using NA- MIC Kit –Part of NA-MIC Outreach to New Applications First Slicer3 svn commit: January 26, 2006

National Alliance for Medical Image Computing Progress in 2009 Numbers 2007 –Subversion Commits: 3,407 –Lines of Code*: 371,428 –Bugs & Features: 154 Submitted 63 Closed –Active Developers † : 33 *: 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 Numbers 2009 –Subversion Commits: 3,224 (11,541 total) –Lines of Code*: 914,466 –Bugs & Features: 336 Submitted 156 Closed –Active Developers † : 68 3D Slicer Version 3.4/3.4.1 –Released May/October, 2009

National Alliance for Medical Image Computing Funding Milestones of 2009 Slicer has Key Role in National Center for Image Guided Therapy (NCIGT – Jolesz, BWH) –Renewed for 5 years ARRA Supplements –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 Extension Modules Allow Distribution of Plug-in Functionality 27 Extensions From NA-MIC Developers, Investigators and Collaborators Command Line, Scripted, Loadable… 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 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

National Alliance for Medical Image Computing 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 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 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 White Matter Anatomy Exploration of White Matter Structures in Language Processing (Lemaire, Golby) –Use Structural, DTI, fMRI

National Alliance for Medical Image Computing 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 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 More Work for 2010 Increased Emphasis on TESTING Increased Use of Extension Modules Emphasis on Python as Scripting, Numeric, and Parallelization Tasks