1. Open Source Workshop MICCAI 2005 Insight Software Consortium (ISC) National Alliance for Medical Image Computing (NA-MIC)

2. Just by choosing where you stand, You alter your destiny Deng Ming-Dao

3. Organization MICCAI 2005 – Jim Duncan, Guido Gerig – Larry Staib, Martin Styner, Delphine Bull, Carolyn Meloling Insight Software Consortium (ISC) – Julien Jomier, Stephen Aylward, Luis Ibanez NA-MIC – Tina Kapur, Steve Pieper, Ron Kikinis

4. MICCAI 2005 First Open Source Workshop at MICCAI – Open Source is a common resource – Open Source fulfills a role in research – Open Source fulfills a role in commercial apps. First Open Access Workshop at MICCAI – Open peer-review process – Full electronic submission

5. Insight Software Consortium (ISC) Not-for-profit organization Mission: Education Academic and commercial institutions Holder of copyrights for ITK, IGSTK, and … Promoter of Open Source Promoter of Open Science

6. Mission of the ISC ISC provides open-science environments and data for developers and users involved in medical image analysis research Users’ and Developers’ Point of ViewISC Provides Does the software work?Dashboards Time and interaction to download and install?Packaging Documentation online and available for download?Documentation Standard Consistent code quality?Coding Standard Active support for individual packages, e.g., email lists?Support Standard How can I learn more about the software?ISC hosts tutorials: SPIE… How can I contribute my research and dataThe Insight Journal Open-source changes too quickly! Backward compatible policy What are open-science is available?The ISC website, The IJ

7. NA-MIC – (NIH-NCBC) NIH Roadmap Initiative Mission – Development of Medical Image Algorithms – Open Source Technologies – Deployment of tools to the Medical Community Driving Biological Problems Promoter of Open Science

8. Open Source Workshop Reproducibility requires sharing – Source code – Images – Parameters Open source – Existing algorithms provide services – New algorithms should be made available to others

9. The Insight Journal Technical work must be reproducible Papers should be publicly accessible Peer-Review process must be open Fully Electronic publishing Not limited to ITK Brought to you by ISC

10. Image Processing Method Algorithm Input Image(s) Parameters Output Image(s)

11. Submission for the IJ Code Input Data Journal Repository Web Site Results Data Author Build Machines PDF doc

12. Insight Journal Manager Author Submits Project DSpace Stores Project Automatic Testing Environment Posts Results Dashboard Submits Entry Reviewer Reviews Project Process Flow Sends Code

13. Benefits of the Insight Journal Allows sharing your Source Code – Faster and larger impact on the community Immediate feedback from Readers and Reviewers – Open Dialog / Forum No Limitations – No page limitations – No limit or charges for color figures – Accepting additional electronic material

14. Benefits of the Insight Journal Indexed by Google Post revisions of papers and code Richer readers experience – Source code available – Original parameters and images available – Reader can try on their own data Accepts practical contributions complimentary to full Journal Papers

15. Benefits of the Insight Journal No Time Constraints – Continuous submission process – Continuous peer-review – Continuous submission of revision (paper/code) Thanks to not using Paper !

16. Credits Julien Jomier – UNC CADDLab Stephen Aylward – UNC CADDLab Zack Galbreath – Kitware Andy Cedilnik – Kitware Bill Hoffman – Kitware Luis Ibanez – Kitware NLM Funding, Dr. Terry Yoo

17. Workshop Response 37 Submissions 90 Reviews by 31 Reviewers 261 Registered Users Anonymous reviews allowed, but none were submitted Reviewers scored – Sensitivity – Helpfulness

18. Reviewers Affiliations Harvard Medical School University of Iowa University of North Carolina German Cancer Research Centre (DKFZ) Georgia Institute of Technology University of Alberta University of Melbourne Kitware

19. Reviewers Affiliations Mayo Clinic MICE Imaging Centre, Toronto Universite catholique de Louvain (UCL) INRA, France SCI Institute – University of Utah Johns Hopkins University University of Pittsburgh Washington University

20. Scoring Papers are scored by taking the average of – review score X reviewer’s score Reviews are scored by readers Reviews are scored by Sensitivity – STAPLE Score from automatic build system

21. http://www.Insight-Journal.org

25. Comparison of output images Publicly available Tests for non-trivial images Reviewers and readers can use it as a first view of the paper. Results Verification

27. Enjoy Open Science

28. Open Access Prize “The Logic of Scientific Discovery” by Karl Popper “Conjectures and Refutations” by Karl Popper For authors and reviewers who contributed to Open-Science

29. Open Access Prize Papers Lydia Ng – Allen Institute Brain Science Casey Godlett – UNC Chapel Hill Gavin Baker – University of Melbourne Reviewers Ingmar Bitter – NIH David Holmes – Mayo Clinic