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Transcript of Open Source Workshop MICCAI 2005 Insight Software Consortium (ISC) National Alliance for Medical...
Open Source Workshop
MICCAI 2005Insight 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 ProvidesDoes the software work? DashboardsTime and interaction to download and install ? PackagingDocumentation online and available for download? Documentation StandardConsistent code quality? Coding StandardActive support for individual packages, e.g., email lists? Support StandardHow can I learn more about the software? ISC hosts tutorials: SPIE…How can I contribute my research and data The Insight JournalOpen-source changes too quickly! Backward compatible
policyWhat 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
AlgorithmInput
Image(s)
Parameters
OutputImage(s)
Submission for the IJ
Code
InputData
JournalRepository
WebSite
ResultsData
Author
BuildMachines
PDF doc
Insight JournalManager
Author
SubmitsProject
DSpace
StoresProject
AutomaticTesting
Environment
PostsResults
Dashboard
SubmitsEntry
Reviewer
ReviewsProject
Process Flow
SendsCode
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
• 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
Enjoy Open Science
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
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