Open Source Software in Image Guided Surgery and New Age of Publishing Luis Ibáñez KITWARE, Inc.

IGSTK The Image Guided Surgery Toolkit

Open Source BSD License Software Development Process

IGSTK Software Process

IGSTK Team Georgetown University UNC Chapel Hill Atamai Canada Kitware * Subcontracts PI STTR – NIH Primary

Design - Implementation Process Surgical Procedure Workflow Analysis Factorizing Components Wiki Page Requirements Wiki Page Design Sandbox Version Code Reviews CVS Commit Maintenance

Traceability – FDA Process Requirements Bugs Bug Tracking Database CVS Commits Logs

Team Coordination

Design Discussions - Wiki

Requirements - Wiki

Agile yet Strict Developers Discussions – Tcon, IM, Mailing List, Wiki Code Reviews CVS Sandbox CVS Main Wiki Proposals Bug Reports

Code Reviews - Wiki

Bugs - CVS Commits linkage

Interaction of Multiple Components Images Geometrical Objects Graphical Representation Visualization Tracking

GUI General Interactions View1 View2 View3 View4 Object Representation Spatial Object Tracker TrackerTool 1 TrackerTool 2 TrackerTool 3 Object Representation

GUI Timing Controls Scene (view1,repr7) (view3,repr9) View1 View2 View3 View4 Object Representation Spatial Object Tracker TrackerTool 1 TrackerTool 2 TrackerTool 3 Object Representation Tick

IGSTK

The Insight Journal

Success Story C. R. Maurer, Jr., R. Qi, and V. Raghavan "A Linear Time Algorithm for Computing Exact Euclidean Distance Transforms of Binary Images in Arbitrary Dimensions“ IEEE - Transactions on Pattern Analysis and Machine Intelligence 25(2): ,

Success Story 2006 – University of Iowa – Hans Johnson & Vamsi Jammalamadaka – Atlas-Based Segmentation – Bottle neck: Distance map computation – Future work: try Maurer’s published method

Success Story February :26 about new Insight Journal submission 12:30 print and read documentation while 12:45 download source code, replace method in their application and compile it 13:00 run on one dataset

Success Story February :03 curse because it could not have possible be computed in only 3 minutes 13:10 Compare with previous results: Do dance of joy because new results are nearly the same as the old ones 16:00 Write an Insight Journal review

The Insight Journal Technical work must be reproducible Papers should be publicly accessible Fully Electronic publishing Not limited to ITK Brought to you by ISC

The Insight Journal Reproducibility requires sharing – Source code – Images – Parameters Open source – Existing algorithms provide services – New algorithms should be made available to others

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

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

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

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 !

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

The Insight Journal