Robarts Training Session

Course Description

The NA-MIC Kit is a free open-source software platform for biomedical researchers and algorithm developers working in the fields of medical image analysis, visualization and image-guided therapy. This NA-MIC Kit Software Workshop is a two-day interactive course allowing scientists and trainees to learn about the NA-MIC Kit, including 3D Slicer, The Visualization Toolkit (VTK), The Insight Toolkit (ITK) and CMake. Participants will receive hands-on training in the end-user applications and software libraries, making this course applicable to both clinical users interested in using the software for their image analysis and visualization tasks, and software developers considering using the NA-MIC Kit as their software platform.

Course Faculty

• Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
• Steve Pieper, Ph.D., Isomics Inc.
• Noby Hata, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
• Danielle Pace, B.CmpH, Robarts Research Institute and The University of Western Ontario

Local Hosts

• Aaron Fenster, Ph.D., Director, Ontario Institute for Cancer Research Imaging Pipeline Platform
• Terry Peters, Ph.D., Robarts Research Institute and The University of Western Ontario

Logistics

• Dates: Wednesday, October 15 - Thursday, October 16, 2008
• Venue: Room 100, London Hall, 1421 Western Road, The University of Western Ontario, London, Ontario, Canada
• The University of Western Ontario on Google Maps
• Driving directions to The University of Western Ontario
• Map of campus

Registration

• In order to maintain a close participant-faculty ratio, space is extremely limited.
• Please register with Sandra Noble-Topham via email (snt [at] imaging.robarts.ca) by Friday, September 26, 2008. Please include your:
  • Full Name
  • Email address
  • Telephone number
  • Lab supervisor
  • University Name
  • Current status (Masters Candidate, PhD candidate, undergraduate, staff member or principal investigator)
  • Any dietary restrictions

Course Requirements

• To participate in this interactive workshop, attendees are required to bring their own laptop with the tutorial software and sample datasets pre-installed.

Sponsors

• 

  National Alliance for Medical Image Computing

• 

  Ontario Institute for Cancer Research

• 

  Imaging Research Laboratories, Robarts Research Institute

Agenda

Arrival: Tuesday, October 14

Time	Wednesday, October 15	Thursday, October 16
08:00-08:30	Breakfast	Breakfast
08:30-10:00	08:30-08:45 Welcome (Aaron, Terry, Steve) Overview over NA-MIC 08:45-10:00 Engineering methodology: (Steve, Nicole, Katie, Junichi?) Extreme programming What is a software engineering methodology, do I need one? The components of the NA-MIC kit software engineering tools: CMAKE, CTEST, CPACK, Dashboards (Barre's Slides) (Jomier's Slides)	08.30-10.00 Slicer3 IGT Slicer 3 IGT capabilities (15 min. Hata) The IGT Toolkit Concept, Architecture, Design Application specific modules: Neuro, MRIg Prostate, Cardiac 3D US IGT Workflows using Neurosurgical Planning as an Example (60 min, hands-on tutorial, by Pace)
10:00-10:30	Coffee Break	Coffee Break
10:30-12:30	10:30 - 11:00 How to use ITK, VTK, XNAT and Batchmake (Steve, Nicole, Katie, Junichi?) ITK (Jomier) (Slides) VTK (Barre) (Slides) KWWidgets (Barre) (Slides) XNAT (Pieper) (Slides) Batchmake (Jomier) (Slides)	S11:00 - 12:30 Slicer3 (Pieper) Overview and Features (Slides) Architecture and Implementation (Slides)	Slicer 3 IGT continued I/O to trackers, devices, and scanners: OpenIGTLink ( 45 min, Hands-on, by Pace) Lego robot tutorial as an example of robot control (45 min, Demonstration, by Pace) Participants do not need to download this tutorial software CUDA-based volume rendering (15 Min, Demonstration, by Hata, Slides) Clinical needs, approach
12:30-1:30	Lunch	Lunch
1:30-4:00	Plug-ins for Slicer 3 (Pujol): Introduction: Plug-ins as a way to interface external programs (Pujol) Programming into Slicer3: How-to make a "hello world" plug-in - Part 1 (Pujol)
4:00-4:30	Coffee Break	Coffee Break
4:30-6:00	3D Visualization(Pujol) EM Segmentation (Pujol)	Plug-ins continued (Pujol) Programming into Slicer3: How-to make a "hello world" plug-in - Part 2 (Pujol) 17.30-18.00 Registration in Slicer 3 (Slides) ‎(Jomier)

Pre-workshop Preparation List

• To be announced