3D Slicer and the NAMIC Kit for IGT Research

1
3D Slicer and the NA-MIC Kit for IGT Research

• Steve Pieper, PhD
• NAC, SPL, NA-MIC, BIRN, NCIGT, Isomics, Inc.

Founder and CEO of Isomics, Inc. a technology
development company that works closely with
multiple research institutions on projects
including NIH grants and software development.
Much of this work is done in collaboration with
the Surgical Planning Laboratory at BWH.
2
Acknowledgments

• F. Jolesz, R. Kikinis, C. Tempany, P. Black, S.
  Wells, CF. Westin, M. Halle, N. Hata, T. Kapur,
  A.Tannenbaum, M. Shenton, E. Grimson, P.Golland,
  W.Schroeder, J. Miller, W. Lorensen, A.
  Yarmarkovich, N. Aucoin, K. Hayes, S. Barre, W.
  Plesniak, D. Marcus, and many more.

3
Goals

• NA-MIC Kit Software and Methodologies for
  Medical Image Computing
• Facilitate Research
• Promote Interoperability
• Stable, Cross-Platform Run Time Environment
• Full set of core features
• Flexible Module Architecture
• Plug-ins added as needed

4
Fully Open, Interoperable Components

• End User Application
• 3D Slicer
• Image Analysis, Visualization, and GUI libraries
• ITK, VTK, KWWidgets
• Large Scale Data Processing Tools
• Batchmake, XNAT, BIRN GRID tools
• Software Engineering Tools
• CMake, Dart, CTest, CPack

http//www.na-mic.org/Wiki/index.php/SoftwareInven
tory
Provided by Pieper, Kikinis
5
Where Does Slicer Fit?

• Shared Platform for Research and Applications
• Ensure Data Compatibility
• Enable Algorithms at Run Time As Needed
• Common Developer Vocabulary
• Consistent User-Centered Interface
• Leverage
• NIH Investment
• Best of Breed Open Source Tools
• Collaborator Expertise
• Unique Environment
• National Scope
• Clinical and Research
• Commercial and Academic

• Slicer is a research platform
• NOT an FDA approved medical device
• NOT finished some parts will work better than
  others

Image provided by A. Golby, F. Talos, P. Black
6
Image/Scene Management

• XML-Based MRML File Stores Scene Description
• Volumes (Images, Label Maps)
• Models
• Hierarchical Affine Transforms
• Scene Data (Cameras, Colors, Fiducials, etc)
• Undo/Redo, Scene Snapshots
• Careful Attention to Coordinate Systems
• Scalar Images
• Diffusion Images
• Time Series (fMRI)
• Visualization

Provided by S. Pieper
7
More Slicer3 Featuresin Development

• Fully Scriptable in Tcl or Python
• Links to scipy, numpy, pylab, matplotlib
• SlicerDaemon
• All Data and API available by connecting to
  socket
• Execution Model
• Very easy to develop plug-in modules that run
  either as shared libraries or command line
  executables
• Experiment Control
• Ties to databases and distributed computing to
  run analyses on large populations
• Informatics Interfaces XCEDE, XNAT, BatchMake
• Much more on the drawing board
• 3D Widgets, DICOM WG23, caBIG

8
Modularity Project

• Keep the base package lean and mean
• Modules have individual identity
• Per-module web site, svn, downloads, mailing
  lists, wiki
• Allow users to assemble their own set of tools
• Customized Bundles by task or application
• Easy to download compatible extensions
• Analogous to Firefox extensions
• Integrate extension builds into
  developer/nightly/release processs
• NITRC Supplement to NA-MIC helping to pay for
  needed infrastructure (Neuroimaging Informatics
  Tools and Resources Clearinghouse)
• NITRC can host neuroimaging projects (gforge
  implementation)

9
Base Features vs. Modules
10
Its all great, but

• A few caveats
• Its a big, distributed group
• Pro Wisdom of the Crowds
• Con Designed by Committee
• Its all research
• Constantly evolving
• Never enough documentation
• Plurality of approaches
• How well we work together will determine the
  impact of our work