AHM2010:NA-MIC Kit Update

Back to AHM 2010

Goals

Information about NA-MIC Kit component developments over the past year so that developers will have an idea of what new features are available for their use.

ITK

• ITK turned 10 years old!
• Slicer currently uses ITK 3.16
• Label image classes, Label map classes, Label map morphology
• Region based Level Sets
• Improvements in Streaming large images
• QuadEdgeMesh spherical registration
  • Rigid (in NAMIC Sandbox)
  • Deformable (Diffeomorphic Demons) (in NAMIC Sandbox)
  • Improvements in the QuadEdgeMesh filter class (in ITK to support the two above).
• Pixel coordinates consistency
• Multi-threaded registration framework (fixes)
  • multi-threaded metrics
  • thread-safe transforms
• Hessian-based shape descriptors
• Fractal dimensions
• FFT based image reconstruction

VTK

• VTK 5.4 released
• vtkWidgets
• VTK ARB formed
• User Voice added to gather community feedback
• VTK Journal
• VTK Edge will be consolidated into VTK
• In progress:
  • VTK 2D Charting
  • Informatics
  • Examples makeover
  • git mirror of VTK

Teem

• Teem 1.11 Soon to be Released
  • release branch being used in slicer3 nightly builds
  • Many improvements and new features described in the Teem 1.11 Change Log Message
• Python wrappers (auto-generated by ctypeslib) now included in teem/python/ctypes; used previously for Two-tensor tractography in Slicer using Python and Teem
• The tenGage kind (for doing convolution-based measurements in tensor fields) now includes direct computation of the fiber curving (tenGageFiberCurving) and fiber dispersion (tenGageFiberDispersion) indices used in Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev BWH)
• New functionality from Thomas Schultz to implement fast crease surface extraction (see his recent TVCG paper [[1]])
• New scale space partices functionality, with applications to lung airway segmentation and white matter skeletonization from DTI
• New applications of scale-space particles for COPD with Raul San Jose (see http://www.airwayinspector.org/)

XNAT

• XNAT 1.4 RC3 available
  • More robust QC modeling via xnat:qcManualAssessorData.
  • New 'columns' variable for REST based listings.
  • LDAP support.
  • Improved memory footprint and efficiency.
  • Refactored Search UI in the listing engine.
• xnatfs provides WebDav access to XNAT instances

GWE

• Interactive experiments' results browser.
• CSV and generated commands dumps and preview.
• Support for LSF and Lava cluster DRMs.
• Ability to override auto-discovered DRMs with configured ones.
• Ability to override default database installation location.
• Function to extract experiments' parameters from text files.
• Operations to delete, pause and resume experiments.
• Recommended to watch: 5 minutes demo video.

BatchMake

• Improvement in the integration of grid computing using condor.
• Semi-Automatic conversion of Slicer modules for batch processing
• Parameter exploration is now possible
• Execution of algorithms are faster

CMake/CPack/CTest/CDash

• parallel ctest (ctest -j)
• cpack
• conversion to cmake in-progress
• linkage between CTest and MIDAS in progress
  • Host large datasets for algorithm validation and performance testing
    • Demonstrated using RegisterImages

3D Slicer

• List of new modules and features (TBD)
  • See here for a list of modules new to 3.5.
• 3.4/3.4.1 release information
• Extension Architecture and Extension Modules
• ARRA Supplement Projects
• Qt Port (lead in to Julien's 8:30 session)
  • Co-existence of KWWidgets and Qt
  • Creation of a subset of the needed Qt widgets
  • Full port in Qt of first modules
  • Design of the core architecture in Qt (plugin mechanism, Command line modules, widget libraries...)
  • Tutorials for the slicer developer community to port modules
  • Gallery and Tutorials
• More info on the Slicer wiki News Page
• multi-camera view in Slicer (endoscopy application)

Other Topics

• Common Toolkit