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

NAMIC Software Development Workshop

December 9-10, 2004Surgical Planning Lab, Brigham and Women’s Hospital 1249 Boylston Street, Boston, MA

National Alliance for Medical Image Computing http://na-mic.org Dec 9-10, 2004

Next 15 minutes…

• NAMIC Background: What, Who, Why• Workshop Objectives• Agenda for Today

National Alliance for Medical Image Computing http://na-mic.org Dec 9-10, 2004

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

National Alliance for Medical Image Computing http://na-mic.org Dec 9-10, 2004

Structure

National Alliance for Medical Image Computing http://na-mic.org Dec 9-10, 2004

NAMIC Background: Who? Algorithms Core

Harvard

Georgia TechUNC

UtahMIT

Segmentation

Registration

Foundational Methods

Structural Features and Statistics

Connective Features and Statistics

3

Attendees of Today’s Workshop

4

5

1

National Alliance for Medical Image Computing http://na-mic.org Dec 9-10, 2004

NAMIC Background: Who? Engineering Core

Isomics

UCLA

Software Integration

Software Engineering

Software Quality

Software Engineering Tools

Data Access Tools

Distributed Computing

Applications

1

Attendees of Today’s Workshop

1

1

National Alliance for Medical Image Computing http://na-mic.org Dec 9-10, 2004

NAMIC Background: Who? DBP Core

Harvard

TorontoDartmouth

UCI

Segmentation

Registration

Foundational Methods

Structural Features and Statistics

Connective Features and Statistics

Attendees of Today’s Workshop

1

National Alliance for Medical Image Computing http://na-mic.org Dec 9-10, 2004

NAMIC Background: Why? Or theNAMIC 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…

How will we execute this vision?•Identify important biological problems•Invent novel algorithms to solve these•Develop persistent, open software implementations•Provide training/documentation/support of software

National Alliance for Medical Image Computing http://na-mic.org Dec 9-10, 2004

Where does this workshop fit in?

National Alliance for Medical Image Computing http://na-mic.org Dec 9-10, 2004

National Alliance for Medical Image Computing http://na-mic.org Dec 9-10, 2004

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

National Alliance for Medical Image Computing http://na-mic.org Dec 9-10, 2004

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

National Alliance for Medical Image Computing http://na-mic.org Dec 9-10, 2004

Agenda for Today• 8:00-8:15am: Introduction and Objectives (Tina Kapur) • 8:15am-8:30am: Open Software Development Philosophy (Luis Ibanez) • 8:30-9:00am: Algorithm development Plans at UNC, MIT, GaTech for Yr1

(Martin Styner, Lauren O'Donnell, Delphine Nain) • 9am-9:10m: Introductions• 9:10am-10:50am: ITK Software Architecture (Luis Ibanez) • 11am-noon: ITK Filters A (Luis Ibanez) • noon-1pm: lunch • 1pm-2pm: ITK Filters B (Luis Ibanez) • 2:10pm-3pm: ITK Segmentation (Luis Ibanez) • 3:10pm-4pm: ITK Segmentation contd.• 4:10pm-5:10pm: ITK & VTK (Luis Ibanez) • 5:10pm-5:30pm: wrap up for day, plans for tomorrow • 6:00pm: Group dinner. Meet at 1249, if you would like to join.