Slicer Update

1. Slicer Update Jim Miller, Ph.D. Steve Pieper, Ph.D.

2. Topics • 2007 Year in Review • Highlights of Slicer3 Features and Application Projects • Plans for This Week and Beyond

3. Progress in 2007 *: 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 • Numbers • Subversion Commits: 3,407 • Lines of Code*: 371,428 • Bugs & Features: • 154 Submitted • 63 Closed • Active Developers†: 33

4. 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

5. 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

6. 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!

7. 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!

8. 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!

9. 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!

10. 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!

11. 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!

12. 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!

13. 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!

14. 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!

15. 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!

16. 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

17. 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

18. 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