NA-MIC National Alliance for Medical Image Computing Slicer Update Jim Miller, Ph.D. Steve Pieper, Ph.D.

National Alliance for Medical Image Computing Topics 2007 Year in Review Highlights of Slicer3 Features and Application Projects Plans for This Week and Beyond

National Alliance for Medical Image Computing 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 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 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 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 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 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 Registration ITK-based Registration Command Line Modules (Lorensen, Blezek, GE) –Rigid, Affine, B-Spline Optimized Multi-Threaded (Aylward, Ibanez, Kitware) Tensor ITK Resampling (Bouix, B udin BWH) Attend the Breakout Session Tuesday at 3!

National Alliance for Medical Image Computing 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 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 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 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 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 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 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 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 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