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