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ITK Architecture

VIEWS: 7 PAGES: 30

									        Open Source
         Workshop

MICCAI 2005
Insight Software Consortium (ISC)
National Alliance for Medical Image Computing (NA-MIC)
Just by choosing where you stand,
You alter your destiny
             Deng Ming-Dao
                     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
               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
     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
                     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 View                        ISC 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 data                       The Insight Journal
    Open-source changes too quickly!                                Backward compatible policy
    What are open-science is available?                             The ISC website, The IJ
          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
       Open Source Workshop
   Reproducibility requires sharing

    – Source code

    – Images

    – Parameters

   Open source
    – Existing algorithms provide services

    – New algorithms should be made available to others
          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
   Image Processing Method

            Parameters



  Input                  Output
             Algorithm
Image(s)                 Image(s)
   Submission for the IJ

           PDF doc
                              Journal
                             Repository
            Code

             Input
Author       Data

            Results   Web             Build
             Data     Site           Machines
                   Process Flow

                       DSpace                       Automatic
                                       Sends         Testing
                                       Code        Environment
                             Stores
                             Project

         Submits                                         Submits
         Project                                         Entry
                    Insight Journal
Author
                       Manager
                                         Posts
                                         Results

                             Reviews
                             Project


                      Reviewer                     Dashboard
    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
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
    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 !
                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
          Workshop Response
   37 Submissions

   90 Reviews

   by 31 Reviewers
   261 Registered Users

   Anonymous reviews allowed, but none were submitted

   Reviewers scored
    – Sensitivity

    – Helpfulness
         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
         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
                  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
http://www.Insight-Journal.org
 Results Verification
• Comparison of output images

• Publicly available

• Tests for non-trivial images

• Reviewers and readers
  can use it as a first view
  of the paper.
Enjoy Open Science
         Open Access Prize
For authors and reviewers who contributed to
Open-Science


    “The Logic of Scientific Discovery”
                             by Karl Popper
    “Conjectures and Refutations”
                             by Karl Popper
         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

								
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