1. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Core 1b – Engineering End-user Platform Steve Pieper Isomics, Inc.

2. National Alliance for Medical Image Computing http://na-mic.org Topics Slicer’s Role in the NA-MIC Renewal 2010 Year in Review Plans for This Week and Beyond

3. National Alliance for Medical Image Computing http://na-mic.org 1 4 2 5 3 Core 1b – Engineering 5 Aims / 5 Platforms Architecture – tools, operating paradigms, reporting mechanisms, integration points End-user platform – interactive methods and information visualization for longitudinal analysis, exploratory data analysis, and translational research Computational platform – stream processing, cloud computing, statistical analysis, informatics, machine learning Data management – non-imaging and derived data, DICOM and cloud services Software engineering and software quality – navigable timeline for revision control, build, test, documentation and release

4. National Alliance for Medical Image Computing http://na-mic.org End-user platform 3D Slicer: a cross platform system for translating innovative algorithms into clinical research applications Developer Needs Clinical Grade IO and UI Rich Utility Libraries Extensible and Reconfigurable Stable Base Easily Deployable Developer Needs Clinical Grade IO and UI Rich Utility Libraries Extensible and Reconfigurable Stable Base Easily Deployable User Needs Easy Install and Upgrade “Standard” Clinical Behavior Consistent Interface Advanced Functionality User Needs Easy Install and Upgrade “Standard” Clinical Behavior Consistent Interface Advanced Functionality

5. National Alliance for Medical Image Computing http://na-mic.org Clinical Grade IO and UI Slicer developers work closely with DBPs on real data and are exposed to clinical state of the art Rich Utility Libraries NA-MIC Kit Extensible and Reconfigurable Loadable Extensions Scriptable GUI Stable Base Nightly Extensions Built Against Latest Slicer Release Slicer Release Relies on Upstream Release (ITK, VTK, etc) Easily Deployable Binary Installers for all platforms Developer Needs

6. National Alliance for Medical Image Computing http://na-mic.org Easy Install and Upgrade Binary installers and Extension Wizard “Standard” Clinical Behavior Adhere to Conventions where Possible Varies by Domain (IGT Navigation vs. Neuroscience Research vs. RT Planning) New Functionality has no “Standard” by Definition Consistent Interface Learning one Slicer Module should help you know how to use other ones Advanced Functionality Main Motivation: you use slicer because nothing else does what you need – we try to make that as painless as possible User Needs

7. National Alliance for Medical Image Computing http://na-mic.org Our Solution: 3D Slicer Focus for NA-MIC Collaborations Platform and Reusable Parts for Wider Community

8. National Alliance for Medical Image Computing http://na-mic.org Impact – 2008-2010

9. National Alliance for Medical Image Computing http://na-mic.org Slicer 3.6 Highlights

10. National Alliance for Medical Image Computing http://na-mic.org Progress in 2010 (Slicer3 only) Numbers 2007 –Subversion Commits: 3,407 –Lines of Code*: 371,428 –Active Developers † : 33 *: find. -iname \*.h -o -iname \*.cxx -o -iname \*.tcl -o -iname \*.java -o -name \*.py | grep -v svn | xargs wc (does not include libraries or modules in external repositories) †: svn log | grep "^r" | cut -d " " -f 3 | sort | uniq | wc Numbers 2009 –Subversion Commits: 3,224 (11,541 total) –Lines of Code*: 914,466 –Active Developers†: 68 3D Slicer Version 3.4/3.4.1 –Released May/October, 2009 Numbers 2008 Subversion Commits: 2,971 (8,317) Lines of Code*: 735,536 Active Developers†: 53 Numbers 2010 –Subversion Commits: 4188 (15,729 total) –Lines of Code*: 925,398 –Bugs & Features: 521 Closed 1046 Total –Active Developers†: 81 3D Slicer Versions 3.6 / 3.6.1 / 3.6.2 –Released June / August / November, 2010

11. National Alliance for Medical Image Computing http://na-mic.org What’s Next? 3D Slicer Version 4.0 –Under Active Development –Developer Beta Binaries Now! –ARRA Supplement for Qt Port Module Porting is Major Goal for 2011 Slicer2 -> Slicer3 was ~80% rewrite Slicer3 -> Slicer4 is ~30% rewrite

12. National Alliance for Medical Image Computing http://na-mic.org Slicer4 Keys to Success Multi-purpose Modules –CLI with Hot Update –Scripted Modules as CLI or Stand-Alone Interfaces “Slicelets” –“.slicer” Extension for scripts that define custom GUI to Slicer functionality Leverage Community Developments (ITKv4, VTK, CTK, NiPy…) Focus on Extensions to Facilitate Collaboration

13. National Alliance for Medical Image Computing http://na-mic.org Extensions Promising Start in Slicer3 –29 Extensions in Nightly Build To be a key part of Slicer4 with CDash@Home –Keep the Core Maintainable –Allow Module Developers to Work with Stable Slicer Release –Nightly Build/Test/Deploy –Independent Repostitory, Wiki, Issues Tracking…

14. National Alliance for Medical Image Computing http://na-mic.org Translational Focus Improved DICOM Support –Local Database –Query / Retrieve / Store –Application Hosting OpenIGT Link and Real-Time Performance Clinical Interfaces –Uncluttered Display –Compare View, Lightbox –Large Format, Multi-Monitor

15. National Alliance for Medical Image Computing http://na-mic.org Frameworks for Solution Types Example: GrowCut Slicer Editor Effect Multiple paint tool interactions Simultaneous viewing of user inputs and segmentation Edit segmentation with additional gestures Framework for other interactive methods User painted gestures Segmentation overlaid with gestures Additional User painted gestures Final Segmentation overlaid with gestures Key Technologies: –GPU Volume Rendering –Registration –Filtering / Segmentation –Diffusion Analysis –Time Series –…

16. National Alliance for Medical Image Computing http://na-mic.org 1 4 2 5 3 Core 1b – Engineering 5 Aims / 5 Platforms Architecture – tools, operating paradigms, reporting mechanisms, integration points End-user platform – interactive methods and information visualization for longitudinal analysis, exploratory data analysis, and translational research Computational platform – stream processing, cloud computing, statistical analysis, informatics, machine learning Data management – non-imaging and derived data, DICOM and cloud services Software engineering and software quality – navigable timeline for revision control, build, test, documentation and release