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Free Open Source Software for IGT

Free Open Source Software for IGT. Ron Kikinis, M.D. Professor of Radiology, Harvard Medical School. Founding Director, Surgical Planning Laboratory, Brigham and Women’s Hospital

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Free Open Source Software for IGT

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  1. Free Open Source Software for IGT Ron Kikinis, M.D. Professor of Radiology, Harvard Medical School Founding Director, Surgical Planning Laboratory, Brigham and Women’s Hospital Principal Investigator, National Alliance for Medical Image Computing (a National Center for Biomedical Computing, part of the Roadmap Initiative), and Neuroimage Analysis Center (a NCRR National Resource Center) Research Director, Image Guided Therapy Program, Brigham and Women’s Hospital

  2. Acknowledgments • F. Jolesz, W. Lorensen, W. Schroeder, C. Tempany, P. Black, K. Hynynen, S. Wells, N. Hata, S. Warfield, CF. Westin, M. Halle, S. Pieper, and many more….

  3. Types of IGT Research • Testing of devices provided by commercial vendors • Can be done in a clinical environment • Modification of existing devices • Requires dedicated research time • New methods • Requires dedicated research time and dedicated personnel

  4. The Two Worlds of IGT • Clinical devices • Government regulated (for protection) • “Freeze” the procedure and devices • Characterize behavior • Document • Research devices • Regulated through research protocols • Frequent modifications • Characterization/testing is an afterthought • Documentation is always behind

  5. IGT Today • IGT has a history of proprietary approaches • Hardware is by default proprietary • Funding agencies often require commercialization which is easier with proprietary approaches

  6. Consequences • Proprietary software and hardware • Locks researchers to a single vendor • Prevents leveraging of the work of other scientists • Graduate students (the work force of science) eternally reinvent the wheel

  7. National Alliance for Medical Image Computing Academic and commercial partners Funded by NIH Leverages other work at the participating sites NA-MIC: A Template ? Provided by Kikinis

  8. What is NA-MICs science? • Computational tools for image analysis (algorithms) • Software engineering methods and applications for image analysis (tools) • Application science

  9. A Public Highway … • “NA-MIC kit” is like a Public Road System: • Provides open source infrastructure • “Driveways” can Lead to Anything: • a Private Facility (commercial product) • a Public Park (FOSS) FOSS= Free Open Source Software Provided by Pieper, Kikinis

  10. BSD style: what does that mean? • Open Source: No restrictions on use • No license fees • You can use the source code to develop a commercial package that you sell. No need to ask for permission. • If you use our software, you are responsible to make sure that you comply with all regulations that apply to the way you use it. • E.g. if you want to use it for clinical trials, you have to apply for the proper authorizations at your institution • You MUST acknowledge our contribution • E.g. Insert a text like the following into the “about” section of your package or product: “This product is based on the 3D slicer software, see www.slicer.org for more information” • You can contribute back to us. It is your choice, if you want to do that and it is our decision, if we will accept it. • BSD=Berkley Software Distribution

  11. The NA-MIC Kit • 3D Slicer: Plattform for delivering image analysis technology to end-users • Several toolkits, other infrastructure, and methodologies • Native support for several plattforms: Windows, Linux, OS X, Solaris Provided by Pieper, Kikinis

  12. 3D Slicer • Application for image analysis and data visualization • Free Open Source Software available for Windows, Linux, Solaris and Mac OS X • Supports a large number of image formats • Google: “slicer 101” for more information

  13. Segmentation Provided by K. Pohl

  14. Overlay Before: After: Rigid Registration Provided by Talos, Pieper et al.

  15. Analysis of Tubular Structures • Diffusion Tensor Imaging • Automatic extraction of anatomically meaningful fiber bundles in the WM of the brain • Cluster Analysis • Rendering outside Slicer using photon mapping Provided by Banks, Shenton, Kindleman, Westin, Bouix, et al.

  16. Tracking E.g. MicroBird Sensor fits on tip of flexible scopes

  17. Release Patch Nightly Continuous Extreme lifecycle Prototype Release X.Y Release X.Y.1 Private Sandbox 2 months Release X.Y.2 NA-MIC Sandbox Slicer 4 months Release X.Y.3 ITK 6 months Development Methodology Testing CMake CTest CPack Dashboard

  18. Tools • Suite of software engineering tools supporting a multi-site development effort • Cmake = multiplatform compilation using native compilers (windows, OS X, Linux, Solaris) • CTest = automatic testing after compilations • Dart2 = web-based management of the development • CPack = Platform sensitive automatic installation of software

  19. CMake • Manage the build process • Find system libraries and code • Compile source code • Assemble resulting binary modules • Create libraries • Construct executables • Enable customization, e.g. • Specify location of source, object code, executables • Build debug or optimized • Do it cross-platform, combinations of • hardware • software • compiler • compiler options • Do it fast • Parallel compilation • Rapid dependency checking CMake is like a universal remote that controls multiple build environments with a single interface. CMake manages complex software development environments – like a universal remote control automatically manages the components of a multimedia system by simply specifying the media type Provided by Schroeder, Cedilnik

  20. Adoption Beyond Medical

  21. NCIGT • National Center for Image Guided Therapy • NIH funded • Leverages NA-MIC software platform

  22. IGT Specific Capabilities • Open Standards are needed for: • Trackers • Scanner control • Navigation systems • Robotic devices

  23. Hardware Standards • USB keys are an excellent example for a successful hardware/software standard: • Devices available from different vendors • Same device works on different computers with a variety of operating systems • Closer to IGT: Opentracker is an emerging BSD licensed package that provides an open interface to several proprietary tracking systems

  24. Recommendations • Free Open Source Software • NA-MIC methodology allows multi-party development and quality assurance • Potential to bridge the gap between research and clinical devices • Open Standards for Hardware interfaces • Computer industry offers good templates: Standardization through ACM and IEEE

  25. Commercial Efforts • Commercialization is the proper channel for distributing clinical devices • Value-added commercialization is the proper mechanism to take advantage of open research • The proposed framework with BSD style license and infrastructure for automated testing lowers the threshold for translational work

  26. IGT Engineering Workshop: ncigt.org Date: October 19-20, 2006. Location: Rockville, MD Open to everybody Attendance limited by size of venue only

  27. For More Information • National Center for Image Guided Therapy www.ncigt.org • Surgical Planning Laboratory www.spl.harvard.edu • National Alliance for Medical Image Computing www.na-mic.org

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