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NAC Engineering Core

NAC Engineering Core. Steve Pieper, Core PI SPL; Isomics, Inc. Overview of NAC Engineering Core. Was BIRN Core, but split per NIH request NAC Engineering Core mBIRN Grant fBIRN Grant (Sandy took lead) Mainly do 3D Slicer development Also sponsored by NA-MIC, NCIGT, R01, SBIR, others….

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NAC Engineering Core

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  1. NAC Engineering Core Steve Pieper, Core PI SPL; Isomics, Inc.

  2. Overview of NAC Engineering Core • Was BIRN Core, but split per NIH request • NAC Engineering Core • mBIRN Grant • fBIRN Grant (Sandy took lead) • Mainly do 3D Slicer development • Also sponsored by NA-MIC, NCIGT, R01, SBIR, others…

  3. Slicer2 • Load Medical Image Data: MR, CT in DICOM, GE, Analyze… • XML-based File Format: MRML (Medical Reality Markup Language) • Interactive Editor: Draw, Threshold, Math Morphology… • Automated Segmenters: EM Segmentation, Fast Marching, Level Sets… • Visualization: Model Building, Stereo Rendering, Animation… • Registration: Manual, ITK, CNI • Measurement: Fiducial-Based, Volumetric, Polyhedral Intersection, Vessel Cross-Section, Osteotomy Planning • IGT: Tracked Probes, Real-Time Images, Robot Control • Additional Application-Specific Features in Modules… • Mature and stable, but becoming difficult to maintain and extend • Needed: • New look and feel • More modularity • Generalized data model

  4. Slicer2 DTI

  5. Slicer2 fMRI

  6. Slicer3 Effort • Collaboration of NAC, NA-MIC, BIRN, NCIGT, Others… • Base Development at BWH, GE, Kitware, Isomics • Module Development at MGH, BWH, UNC, Utah, MIT, UCLA, UCSD…

  7. Near Term Plans • 3D Slicer 2.7 Release Candidate • February 2007 • Bug fixes, performance enhancements • 3D Slicer 3.0 Base Release • March 2007 • Essential feature (load/save, view, transforms, models…) • 3D Slicer 3.1 Release • June 2007 • Application modules (DTI, EMSegment)

  8. Longer term plans • Slicer3 Informatics • XNAT (mBIRN), HID (fBIRN), MIDAS (Kitware) • Query Atlas (mBIRN, fBIRN) • Execution Model for Grid Computing (mBIRN, NA-MIC) • DICOM / IHE Clinical Workflows (pending with Northwestern) • FEM Meshing / Visualization (Iowa, ongoing) • DTI (NAC, NA-MIC, mBIRN) • Interoperability (NAC, mBIRN) • FreeSurfer, FSL, MATLAB, NumPy… • Image Guided Therapy (NCIGT, NAC)

  9. Slicer3 Execution Model • Standardized command line syntax and exchange of data (parameters, volumes, models, seed points…) • Slicer3 auto-generates GUI • Modules are “just executables” • (but they can also be shared libraries) • Modules can be written in a variety of languages/toolkits (ITK, VTK, Tcl, Python, MATLAB, C, C++…) • Modules can be used for scripting, batch processing • Simple wrappers to translate syntax can allow interoperability

  10. Slicer 2.6 Functionality: FreeSurfer

  11. BIRN Query Atlas in Slicer3 • Re-Architecture of the QueryAtlas • Advanced Label Features Built-In • Real-Time Interaction with Labels • “Right Click” on Models and Images to Initiate Queries • Based on NA-MIC Software Engineering Methodology • Anatomy-Based Access to Web Resources • Integrates with BIRN IT Efforts • Auto Convert and Load BIRN Data • Leverages mBIRN Data Formats and Analysis (FreeSurfer) • fBIRN is Building Functional QueryAtlas Integrated with mBIRN QueryAtlas

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