1. NAMIC Software Development Workshop
February 17-18, 2005
BIRN CC, UCSD

2. Next 15 minutes… NAMIC Background: What, Who, Why Workshop Objectives
Agenda for Today

3. NAMIC Background: What?
Supported by NIH
One of four NCBCs
National Center for Biological Computing
PIs: Ron Kikinis, Steve Wong
Unique in strong engineering emphasis along with science: value associated with software persistence
7 Cores, 13 Sites

4. Structure

5. NAMIC Background: Who? Algorithms Core
Harvard
MIT
Utah
Segmentation
Registration
Foundational Methods
UNC
Georgia Tech
Structural Features and Statistics
Connective Features and Statistics

6. NAMIC Background: Who? Engineering Core
UCLA
Software Engineering
Software Engineering Tools
Software Quality
Isomics
Software Integration
Data Access Tools
Distributed Computing
Applications

7. NAMIC Background: Who? DBP Core
UCI
Harvard
Segmentation
Registration
Dartmouth
Foundational Methods
Toronto
Structural Features and Statistics
Connective Features and Statistics

8. NAMIC Background: Why? Or the NAMIC Vision
Student reads a paper that references a NAMIC algorithm… goes to web site .. uses software implementation of algorithm to see results on own data…

9. Where does this workshop fit in?

11. Workshop Objectives
Provide a hands-on introduction to software development using NAMIC Kit V0
ITK 1.8
Slicer 2.4
Introduce team to NAMIC ITK and Slicer Experts
Start exchange of feedback between algorithm, engineering, and dbp cores

12. Desired Outcome over next 2-3 months
Use one of the tools in your own work, in collaboration with an engineering core member
Provide feedback on the fit of the tool with your research
Bring some of this experience with you to the AHM in SLC in Feb

13. Agenda for Day 1: Slicer
9-9:30am:Welcome and Objectives(Ron Kikinis, Tina Kapur)
9:30-10:15am: NA-MIC Software Engineering Methodology and Resources (Dan Blezek)
10:15-10:30 Break
10:30-11:15am Developers tools (Steve Pieper)
11:15-12noon: Slicer Overview, Slicer Demo, Slicer Build and Deploy System (Steve Pieper)
noon-1pm: lunch
1-1:30pm: DTI Processing Demo (Raul San Jose)
1:30-2:30 Slicer Architecture, and Compiling Custom Modules (Steve Pieper)
2:45-3:00 Break
3:00-3:45pm: Integrating ITK/VTK modules in Slicer Slicer and ITK I/O factory generic readers module (Raul San Jose)
3:45 - 4:30 ITK/Slicer Integration Exercises
4:30-5pm: Introduction to the UCSD Data Grid Infrastructure (Mark James)
5-5:15pm: wrap-up (Tina Kapur)

14. Agenda for Day 2: ITK 9:00am-noon: ITK Architecture (Luis Ibanez)
noon-12:30: lunch
12:30-1:30pm: ITK Filtering (Luis Ibanez)
1:45-3pm: ITK Segmentation (Luis Ibanez, Josh Cates)
3-3:20pm: break
3:20-4:50pm: ITK Image Registration (Luis Ibanez)
5pm-6pm: Intro to VTK & Combining ITK and VTK (Luis Ibanez)
6pm: Wrap-up (Tina Kapur)