Miccai 2008 Tutorial

Interfacing third-party software with the NA-MIC open-source toolkit

This tutorial is part of the 11th International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2008.

Academic Objectives

The emergence of increasingly sophisticated mathematical models, image analysis and visualization tools that have followed the rapid development of new medical imaging technologies has led to a better understanding of organ functions in human health and disease. For the past four years, the National Alliance for Medical Image Computing (NA-MIC), one of the seven National Centers for Biomedical Computing (NCBC), part of the NIH Roadmap for medical research, has focused its efforts on the conversion of scientific advances from the biomedical imaging community into an open-source toolkit, so as to improve the availability and deployment of advanced software tools on a national scale. The purpose of this tutorial is to provide the members of the MICCAI community with a practical experience of the image processing and 3D visualization capabilities of the National Alliance for Medical Image Computing (NA-MIC) open-source software toolkit.

Syllabus

The workshop combines introductory lectures on the software components of the NA-MIC kit, with hands-on tutorial sessions that guide the participants through the integration of the open-source tools with third-party software. Participants will be able to interface their own algorithms with the NA-MIC kit to facilitate greater interoperability of advanced medical image analysis software tools. This course is intended for scientists and engineers of the medical image analysis community.

Agenda 12 pm - 5 pm

• 12:00-12:10 pm: Introduction and Goals of the Workshop (Sonia Pujol)
• 12:15-12:30 pm: Presentation of NA-MIC (Steve Pieper)
• 12:30-12:45 pm: Overview of the NA-MIC Methodology and Open-Source Software Toolkit (Sonia Pujol)
• 12:30-1:30 pm: Hands-on Session 1: 3D Data Loading and Visualization (Sonia Pujol)
• 1:30-1:45 pm: Coffee Break
• 1:45-2:15 pm: Introduction to the Execution Model in 3D Slicer (Jim Miller)
• 2:15-3:30 pm Hands-on Session 2: Integrating the NA-MIC kit with an External Program (Sonia Pujol)
• 3:30-3:45 pm: Coffee Break
• 3:45-4:15 pm:Hands-on Session 3: Running Tests with the NA-MIC kit (Sonia Pujol)
• 4:15-4:45 pm: Panel Discussion and Conclusion

Course Faculty

• Sonia Pujol, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Department of Radiology, Brigham and Women's Hospital, Boston, MA.
• Steve Pieper, Ph.D., Isomics Inc., Cambridge, MA.
• Jim Miller, Ph.D., Visualization & Computer Vision, GE Research, Niskayuna, NY.

Logistics and Registration

• Date: Wednesday September 10, 2008
• Time: 12-5pm
• Location: Kimmel Center, Room 802, New-York City University
• Participants are required to come with their own computer (PC, Linux or MacOS).
• Attendance is limited to 25 participants. To sign-up for this event, please register through the MICCAI 2008 website and send an e-mail with the subject line 'MICCAI 2008: NA-MIC toolkit tutorial' to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu) with the following elements
  • contact information: name, title, affiliation and address
  • category: user or developer,
  • laptop characteristics: OS, RAM, Processor

Pre-Workshop Preparation

The workshop is a series of hands-on sessions. Please complete the Developer Prerequisites in advance of the workshop.
Note: Building Slicer can take up to 2 hours. We recommended the following configuration: Windows XP, Linux (x86 or x86_64), Mac OS (ppc or Intel), 2 GB of RAM and a dedicated graphic accelerator with 128 MB of on board graphic memory. Please contact the Slicer Users mailing list for support and questions related to the software.