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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
NAMIC-Kit Update
Will Schroeder
Jim Miller
Bill Lorensen
National Alliance for Medical Image Computing http://na-mic.org
Progress This Year
Project
Rela
tive
E
ffort
Current open-source NAMIC Kit components
National Alliance for Medical Image Computing http://na-mic.org
Slicer 3
• Usage– End user application– Algorithm delivery platform– Application development framework
National Alliance for Medical Image Computing http://na-mic.org
Slicer (cont.)
• Past Year (New system)– Design discussions (2005)– Core Architecture (Feb. 2006)
• MRML• Event processing• Images, models, fudicials, transforms
– Plug-in Modules (May 2006)• Threaded GUI• Command-line Modules• Command-line processing
National Alliance for Medical Image Computing http://na-mic.org
Slicer (Past Year)
• More on the wiki: Slicer3:Status_Summary• MRML• Slices• 3D View• Data GUI• Volume processing• Models• Transforms• Application GUI• Fiducials• Execution model• Editor• Build / packaging• DART Dashboard / testing
National Alliance for Medical Image Computing http://na-mic.org
Slicer (Past Year)
• Modules– ModelMaker– Fiducials– FreeSurfer
readers– EM Segmenter– DTMRI
National Alliance for Medical Image Computing http://na-mic.org
Slicer 3 Modules
• CommandLineModule– Add
– AffineRegistration
– BSplineDeformableRegistration
– CheckerBoard
– ConfidenceConnected
– CurvatureAnisotropicDiffusion
– GEDicom2NRRD
– GradientAnisotropicDiffusion
– GrayscaleFillHoleImageFilter
– GrayscaleGrindPeakImageFilter
– GrayscaleModelMaker
– HistogramMatching
– ImageReadDicomWrite
– LinearRegistration
– MedianImageFilter
– OtsuThresholdImageFilter
– OtsuThresholdSegmentation
– ResampleVolume
– Subtract
– VotingBinaryHoleFillingImageFilter
National Alliance for Medical Image Computing http://na-mic.org
Slicer
• Futures– (Much) more
of the same– Refine GUI– Usability
• Undo/Redo• Save/Restore scenes
– Many new modules– More testing– Other data types– Performance– Hierarchies of data– Large data / grid processing– More clinical workflows
• Wiki: Slicer3:Developers• Wiki: Wiki/index.php/Slicer
National Alliance for Medical Image Computing http://na-mic.org
KWWidgets
• Usage– Cross-platform GUI with open source license
• Past year– New widgets– Work flow support– File/directory browser
• Futures– Tracing (for testing)– Registration inspection widget– Camera control widget– Interface to ITK (spatial objects)– Cleanup
• Kwwidgets.org
National Alliance for Medical Image Computing http://na-mic.org
CPack
• Usage:– Package and deploy cross-platform software
integrated with CMake• Past Year
– Brand new tool– Supports Windows, Linux, Mac
• Futures– Improved packaging– Advanced packaging and deployment– Packaging Slicer modules
• cmake.org
National Alliance for Medical Image Computing http://na-mic.org
CMake
• Usage– Cross-platform build management
• Past year– Slicer CMake configuration– KDE deployment and support– Better Mac OSX, Win64 support
• Futures– Better NAMIC tool support (e.g., module
integration)– External library integration
• cmake.org
National Alliance for Medical Image Computing http://na-mic.org
ITK – Insight Toolkit
• Usage:– Image processing and analysis (segmentation and
registration)• This year
– Bug fixes / Slicer integration– Fixed deployment issues– Data orientation– Probability distributions– Data I/O (DICOM, NRRD, MRML)
• Futures– DTI representation/processing– Statistics refactoring– IDL language binding– Pre-compiled headers
• itk.org
National Alliance for Medical Image Computing http://na-mic.org
VTK
• Usage– Image, volume, surface display and processing– Event processing– 3D human/computer interaction
• This year– Bug fixes– 3D Widgets– Slicer 2.x integration with VTK 5.0
• Futures– DTI fiber bundles– GPU-based volume rendering– Additional widgets– AMR / large data support
• vtk.org
National Alliance for Medical Image Computing http://na-mic.org
DART
• Usage– Testing/dashboard
server• This year
– Deployment– Base features– User accounts– Notifications– RSS– Bug fixes– Documentation
• Futures– Enterprise deployment
• na-mic.org/Wiki/index.php/Dart2Summary
National Alliance for Medical Image Computing http://na-mic.org
Insight Journal
• Open access publication– Supports publications, software and
data– Open science (reproducibility)– Open peer review– Continuous revision of articles, code,
and reviews
National Alliance for Medical Image Computing http://na-mic.org
ISC/NAMIC Workshop on Open Science MICCAI 2006
National Alliance for Medical Image Computing http://na-mic.org
Insight Journal
• Used as gateway to receive software submissions– ITK
• Futures– Slicer modules ?
• insight-journal.org
National Alliance for Medical Image Computing http://na-mic.org
BIRN• Slicer / Grid Interface
– Provide accessto Grid-basedinfrastructures
– Enable researchersto store largecollections offederated data
Grid Execution Module
Slicer
National Alliance for Medical Image Computing http://na-mic.org
BIRN – Time Frame
Curre
nt
May
, 200
7
Augus
t, 20
07
Testing of Slicer3 module
Monitoring portlet
Incoporation into NA-MIC kit
Mar
ch, 2
007
Testing of Grid
Interface prototype
National Alliance for Medical Image Computing http://na-mic.org
Other – Large Data Processing• LONI
– The LONI Pipeline is a simple graphical environment for constructing complex scientific analyses of data
– Revamped version 4– Slicer integration proceeding (Slicer can
query pipeline for list of required parameters) – http://www.loni.ucla.edu/Software/
• BatchMake– Cross platform tool
for batch processing of large amount of data– Can process datasets locally or on distributed systems using Condor– Script driven– Considering Slicer integration– Batchmake.org
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