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