1. Surgical Planning Laboratory Brigham and Women’s Hospital Boston, Massachusetts USA a teaching affiliate of Harvard Medical School 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. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 3 Types of IGT Research 1.Testing of devices provided by commercial vendors Can be done in a clinical environment 2.Modification of existing devices Requires dedicated research time 3.New methods Requires dedicated research time and dedicated personnel

4. ©2006 Surgical Planning Laboratory, ARR Slide 4 The Two Worlds of IGT Clinical devices –Government regulated (for protection) 1.“Freeze” the procedure and devices 2.Characterize behavior 3.Document Research devices –Regulated through research protocols 1.Frequent modifications 2.Characterization/testing is an afterthought 3.Documentation is always behind

5. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 7 NA-MIC: A Template ? Provided by Kikinis National Alliance for Medical Image Computing Academic and commercial partners Funded by NIH Leverages other work at the participating sites

8. ©2006 Surgical Planning Laboratory, ARR Slide 8 What is NA-MICs science? Computational tools for image analysis (algorithms) Software engineering methods and applications for image analysis (tools) Application science

9. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 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”www.slicer.org 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. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 13 Segmentation Provided by K. Pohl

14. ©2006 Surgical Planning Laboratory, ARR Slide 14 Rigid Registration Overlay Before: After: Provided by Talos, Pieper et al.

15. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 16 Tracking E.g. MicroBird Sensor fits on tip of flexible scopes

17. ©2006 Surgical Planning Laboratory, ARR Slide 17 Development Methodology 6 months 4 months 2 months ReleasePatchNightlyContinuous Release X.Y Release X.Y.1 Release X.Y.2 Release X.Y.3 Extreme lifecycle Dashboard CMake CTest CPack Testing Private Sandbox NA-MIC Sandbox Slicer ITK Prototype

18. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 20 Adoption Beyond Medical

21. ©2006 Surgical Planning Laboratory, ARR Slide 21 NCIGT National Center for Image Guided Therapy NIH funded Leverages NA-MIC software platform

22. ©2006 Surgical Planning Laboratory, ARR Slide 22 IGT Specific Capabilities Open Standards are needed for: –Trackers –Scanner control –Navigation systems –Robotic devices

23. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 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. ©2006 Surgical Planning Laboratory, ARR Slide 27 For More Information National Center for Image Guided Therapy www.ncigt.orgwww.ncigt.org Surgical Planning Laboratory www.spl.harvard.edu www.spl.harvard.edu National Alliance for Medical Image Computing www.na-mic.orgwww.na-mic.org