Relative Roles Core1a Core 1b Core2

Introduction

Based on the experiences of the last 5 years, the role of the Driving Biological Projects (DPBs) in NA-MIC includes the following:

• Willingness to adopt the NA-MIC Kit
• Willingness to use DBP funds to hire at least one computer science person into the DBP to enable translational efforts.

An important mechanism for wide dissemination of the NA-MIC software infrastructure is the NA-MIC Kit. The Introduction for the NA-MIC Kit describes the software included in the NA-MIC Kit as follows:

• It is our intention to include in the NA-MIC kit only software that is supported and comes with a BSD style license.

Based on this background and on conclusions drawn from experience gained during the first six years of operation, the following guidelines describe the role of the 3 main cores of NA-MIC.

Overall objective

The objective of NA-MIC is to establish, at a national level, an open-source software and computing infrastructure to facilitate medical research that relies on image analysis. The infrastructure will support experimental biomedical and behavior research utilizing medical image computing (applications of medical image computing) as well as support fundamental research in medical image computing itself (algorithms, data structures, computing platforms). This infrastructure includes a set of open source software tools for medical image computing along with the necessary supporting software development environment (source code repositories, bug trackers, dashboards, build environment, mailing lists, web site, wiki). The infrastructure is designed to support a range of biomedical and behavior research applications.

The NA-MIC Kit is the foundation of this infrastructure, providing an end-user application (Slicer3), batch processing tools for large scale experiments (BatchMake, GridWizard), and PACS like infrastructure (XNAT) to support biomedical and behavior researchers. The NA-MIC Kit also includes ITK, which is an extensive set of libraries for image analysis, visualization tools in VTK, and a layered plug-in architecture for Slicer3 to support research in medical image computing. All the components of the NA-MIC kit are distributed under a BSD style license free of restrictions.

All the NA-MIC participants will use NA-MIC funding exclusively for work in the NA-MIC kit environment.

Core 1a: Algorithms

NA-MIC funding in the algorithm core is used for work research and development of algorithms in the NA-MIC Kit. Algorithms will be driven by the specific needs of the DBP's, but with a preference for generalizable solutions as opposed to algorithms that are only useful in a particular subdomain. The plan for Core 1a development is that Core 1a sites should implement algorithms in ITK and integrate into Slicer3 via the plug-in modules. Core 1a participants are expected to request specific API's, data structures and facilities from Core 1b to support this work.

Core 1b: Engineering

Participants in this core are concentrating on developing the NA-MIC kit as a platform. The platform will provide the libraries and API's needed by Core 1 to implement their algorithms and the user interfaces needed by Core 2 to make use of the tools. Core 1b participants will consult regularly with Core 1a sites, the Core 1a PI, and the NA-MIC PI in order to establish needs for software infrastructure. Major infrastructure developments will be documented on the Wiki and publicized, by email, to the site PI's.

Core 2: DBP's

Core 2 researchers serve as representatives of their fields and should make algorithm and tool requests that serve not only to fulfill their current research needs, but also to benefit the larger community of users. The DBP's are responsible for developing and modifying NA-MIC-Kit applications to meet their specific needs. Thus, third generation DBP's will use the NA-MIC funding to hire an engineer or software developer who is qualified to work with the Slicer 3 application and will help you to use the tools developed by the Algorithm Core to perform biomedical research. It is expected that Core 2 will produce working end-to-end solutions for a specific problem, publish scientific papers that illustrate the use of such solutions, develop tutorials and sample datasets for each solution, and finally, organize workshops (or similar) to disseminate these solutions to their community.