National Alliance for Medical Image Computing http://na-mic.org

Slicer3 Status Update

National Alliance for Medical Image Computing http://na-mic.org

Overview

• Where do we want to go?

• Where have we been?

• Where are we?

• What’s our plan?

• What’s underway?

National Alliance for Medical Image Computing http://na-mic.org

Where do we want to go?

• June 9 8:30 – 5:00, Satellite Event to the Organization for Human Brain Mapping 2007 (Chicago)

• Diffusion MRI Neuroanatomy, MR Physics, Clinical Applications, Mathematics, Processing and Visualization

• Hands On Exercises with 3D Slicer 2.6• Outcome

– Most Attendees Stayed Late for Q&A, Extra Demonstrations

– 100% reported they would recommend the workshop to others

– 50% are planning to apply the tools and information they learned to their own work

• We want to migrate to these events to Slicer3

– New Algorithms– Cleaner Design

50 registered from 9 countries: USA, New Zealand, Canada, Netherlands, England,

Germany, Korea, Czech Republic & Belgium

13 states within the US: Georgia, Utah, New York, Wisconsin, Hawaii, California, Oregon,

Illinois, Ohio, Minnesota, Pennsylvania, Indiana & Michigan

40 different laboratories including 2 NIH institutes

Fields of expertise representative of the NAMIC collaboration- basic and clinical

neurosciences, physics, image processing and computer science

National Alliance for Medical Image Computing http://na-mic.org

What other goals?

• Make the NA-MIC Kit indispensable for Medical Image researchers (e.g. DBP Users)– Install on your new computer like

cygwin or firefox

• Powerful, Productive Platform for Developers

• Reliable, Usable, Documented…

National Alliance for Medical Image Computing http://na-mic.org

What is Slicer3?

• Total Rework of 3D Slicer– At least 80% of code rewritten

• Draws on Distributed Developer Community

– Kitware, Inc., GE Research, Isomics, Inc., BWH, UCLA, UCSD, UIowa, MIT, GaTech, UNC, U Utah, MGH, UCI, Harvard, WashU, JHU…

– NAC, NCIGT, NA-MIC, mBIRN, fBIRN

National Alliance for Medical Image Computing http://na-mic.org

Where have we been?

• First slicer3 discussions were held here 2 years ago– June 28, 2005

• SVN Revision 1 16 months ago – Jan 26, 2006– 3672 commits as of June 24, 2007

• About a dozen slicer3 1-2 day retreats– At SPL, MIT, Kitware…

National Alliance for Medical Image Computing http://na-mic.org

Where are we?

• Development “ecosystem”– repository, dashboard, mailing lists, bug

tracker, wiki…• Slicer3 Betas

– Base GUI, Slice/Model Interaction, Scene Load/Save, Volumes, Models, Transforms…

– Basic Set of Modules for Registration, Filtering, Editor, Model Building…

• Application Modules– EMSegmenter, Diffusion Processing, Image

Guided Therapy, Meshing, Microscopy…

National Alliance for Medical Image Computing http://na-mic.org

What’s the plan?

• Working with DBPs to Apply Slicer3

• Training Core Creating First Tutorials

• Slicer3 Release Schedule– To be determined at this meeting

• NA-MIC Renewal Needs– Application Publications with New

Algorithms Implemented in NA-MIC Kit

National Alliance for Medical Image Computing http://na-mic.org

What’s Underway? Lots!

• Algorithm Interfaces– Expanded Execution Model with MRML Scene I/O– Integrated scipy and matplotlib– SlicerDaemon Scalar/Vector/Tensor interface to MATLAB– Internal Modules for dMRI

• MRML– Diffusion Volumes, Fiber Bundles, Model Hierarchies, Scene Snapshots and

Clips, Performance Optimization…• GUI

– Style Guidelines, Cine/FilmSheet Slice Displays, Icons, Module Interfaces, File Browser, Editor…

• Large Scale Computing– BatchMake, BIRN XNAT, QDEC Statistics…

• Application Areas– Neuro Segmentation, Lesion Analysis, Diffusion Imaging, Vascular Simulation,

Prostate Interventions, Robotics, Neurosurgery, Astronomy, Microscopy, Radiology Review, Joint Biomechanics, Radiation Treatment Planning…