Slicer Update
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Transcript of Slicer Update
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Slicer Update
Jim Miller, Ph.D.
Steve Pieper, Ph.D.
National Alliance for Medical Image Computing http://na-mic.org
Topics
• 2007 Year in Review
• Highlights of Slicer3 Features and Application Projects
• Plans for This Week and Beyond
National Alliance for Medical Image Computing http://na-mic.org
Progress in 2007
• Numbers– 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†: svn log | grep "^r" | cut -d " " -f 3 | sort | uniq | wc
National Alliance for Medical Image Computing http://na-mic.org
Current State
• Major Functional Blocks are Implemented– MRML, IO, Module Support, GUI, Volume
Rendering
• Several Modules Becoming Usable– EMSegmenter, Diffusion Image Analysis,
Registration, Informatics, QueryAtlas, IGT, Editor, Meshing, Editor, Python
• Bugs and Performance are Still Major Issues
National Alliance for Medical Image Computing http://na-mic.org
Base Features
• Linux (32/64), Mac (ppc/x86), Win32
• All-in-one build and test script
• Nightly builds and tests
• Doxygen/Wiki Developer Docs
• Basic Developer and User Tutorials
National Alliance for Medical Image Computing http://na-mic.org
Volume Rendering
• VTK Hardware and Software Based– Selectable Volume mixed
with Opaque Geometry– Flexible Threshold,
Lookup Table, Cropping, and Interactive Performance Options
• Andy Freudling (BWH) with Lisa Avila and Sebastien Barre (Kitware)
• See Andy for a Demo!
National Alliance for Medical Image Computing http://na-mic.org
EM Segmenter
• Complete Reimplementation of slicer2 based code in slicer3
• Now contains complete registration and segmentation framework
• Kilian Pohl (MIT/BWH) and Brad Davis (Kitware)
• Attend the breakout session at 4!
National Alliance for Medical Image Computing http://na-mic.org
Diffusion Tools
• Core Infrastructure (Yarmarkovich, Isomics; O’Donnell & San Jose Estepar, BWH)
– DWI, DTI, FiberBundles in Scene– Fully load/save including all vis
parameters– DICOM to NRRD (Tao, GE)– Tensor Estimation– Scalar Invariant Volumes– ROI Tractography
• Rician Filtering (Gouttard, Utah)• Stochastic Tractography (Ngo,
MIT)• All Day Breakout Wednesday!
National Alliance for Medical Image Computing http://na-mic.org
Registration
• ITK-based Registration Command Line Modules (Lorensen, Blezek, GE)– Rigid, Affine, B-Spline
• Optimized Multi-Threaded (Aylward, Ibanez, Kitware)
• Tensor ITK Resampling (Bouix, Budin BWH)
• Attend the Breakout Session Tuesday at 3!
National Alliance for Medical Image Computing http://na-mic.org
mBIRN Informatics
• XNAT Web Database of Neuroimages (Marcus, WashU)
• Query, Design, Estimate, Contrast of Population Statistics (Greve, MGH)
• Web Queries to Identify Population
• Population GLM Statistics Run on Grid
• Analysis Results Open in Slicer3 or Interactive Visualization and Plotting (Aucoin, BWH)
• Welcome Dan and the Wash U team to NA-MIC!
National Alliance for Medical Image Computing http://na-mic.org
Query Atlas Features
• Integrated Ontology / Anatomy / Statistics System Volumes and Models Labeled with Controlled Vocabulary
– Co-Registered Individual or Population Statistics
• High Performance Interactive Picking and Labeling
• Launch Web Queries Using Anatomy, Demographic, Diagnostic & Behavioral Terms
• Integrated with BIRN Informatics (Plesniak, BWH; Pieper, Isomics)
• See Wendy or Steve for a Demo!
National Alliance for Medical Image Computing http://na-mic.org
IGT
• Several Groups have NIH Funding to do Slicer3-based Image Guided Therapy
– NCIGT Neurosurgery, Prostate, (Hata, Lui, Tokuda, BWH)
– IGSTK Liver RF Ablation (Cleary, Yanic, Cheng, Georgetown; Ibanez, Kitware)
– NA-MIC Protstate Robot (Fichtinger, Gobbi, Queens; Kazanzides, Csoba, JHU)
– Neuroendoscopy ( Barre, Kitware)
• Real-Time Tracking and Images Needed
• This is very cool!
National Alliance for Medical Image Computing http://na-mic.org
Editor
• General Purpose Label Map Editor– Paint and Draw Tools with Integrated
Thresholding (Pieper, Isomics)
– Level Tracing Auto Segmentation (Miller, GE)
– Clean GUI Based on User Centered Design Process (Plesniak, BWH)
– Module Tool Implementation to Plug in Additional Effects
• There’s still a lot of work to do!
National Alliance for Medical Image Computing http://na-mic.org
Meshing• Workflow to go from CT to FE
Mesh - IA-FEMESH– MIMX Infrastructure
(Grosland, Magnotta, UIowa)– VTK Unstructured Grid
Infrastructure (Kitware)– Voxel Meshing (Magnotta)
and Hexahedral Mapping (Magnotta, Shivanna)
– Slicer Implementation (Lisle, Isomics)
• Additional Benefits– Mesh Infrastructure in MRML– VTK 3D Widgets in Slicer3
• See Curt for a Demo!
National Alliance for Medical Image Computing http://na-mic.org
Python
• Leverage the Scientific Python Community
– Numpy Provides Powerful Interactive Numerical Processing
– MATPLOTLIB Provides MATLAB-Like Publication Quality Plotting
– Variety of Utilities in Scientific Python (scipy)
• Python/Tcl/VTK Bridge– Direct Pointer Access to Slicer
Volumes (Blezek, Mayo/GE/Isomics)
• Python Based Modules– VMTK - Vascular Modeling Toolkit
(Antiga, Mario Negri Institute)
• See Dan and Luca for a Demo!
National Alliance for Medical Image Computing http://na-mic.org
Major Projects for 2008
• Increased Focus on Applications and Community Involvement– Slicer3 is Open for Business!
• Modularity Project– Make the Slicer Base “Lean and Mean”– Expand ModuleFactory for GUI Modules– NITRC (gforge-based) Developer Site
• Event Broker– Replace AddObserver Calls with
National Alliance for Medical Image Computing http://na-mic.org
Modularity Project
• Goals– Address Scalability for New Modules– Only Load what YOU Need– Improved Testability and Efficiency
• Firefox Analogy– Slicer3 Base as has well defined set of supported
functions (volumes, models, transforms… are like text, forms, images, tables)
– Modules/plugins can be downloaded from independent servers
• Project is Underway (Terry Lorber, Alex Yarmarkovich) with Support from NITRC
National Alliance for Medical Image Computing http://na-mic.org
Modularity Targets
• Benefits– Slicer3 Base becomes streamlined and
efficient with clear scope– Modules have distinct identity (web site, wiki,
svn…)
• Features– Integrated with build, test, and package
systems (nightly builds of Base plus compatible Modules available for download)
– Easy for Users to Browse/Install Module Packages