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

• 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
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
  ODonnell 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
• Theres 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