Relative Roles Core1a Core 1b Core2

Introduction

Based on the experiences of the first NA-MIC funding cycle, the role of the Driving Biological Projects (DPBs) in NA-MIC includes the following prerequisites:

• 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 conditions for inclusion of software in the Kit are described in the Introduction to 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 our experience during the first NA-MIC funding cycle, the following guidelines are beginning to emerge regarding the role of the 3 main cores of NA-MIC for the renewal period.

Overall objective

The objective of NA-MIC is to establish, at the national level, an open-source software and computing infrastructure to facilitate medical research that relies on image analysis. It is envisioned that the infrastructure will support experimental biomedical and behavioral research with advanced software applications in medical image computing, as well as fundamental research in medical image computing, itself (algorithms, data structures, computing platforms). This infrastructure will include 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 will be designed to support a wide range of biomedical and behavioral research applications.

The NA-MIC Kit is the foundation of this infrastructure and provides an end-user application (3D Slicer), batch-processing tools for large-scale experiments (iPython), and a PACS-like infrastructure (XNAT and DICOM) to support biomedical and behavioral researchers. The NA-MIC Kit also includes The Insight Segmentation and Registration Toolkit (ITK), which is an extensive set of libraries for image analysis developed with funding from the National Library of Medicine for its Visible Human Project, visualization tools in VTK, Qt for user interfaces, and a layered plug-in architecture for 3D Slicer to support research in medical image computing. All of the components of the NA-MIC Kit are distributed under a BSD style license free of restrictions.

All of 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 Algorithms Core is used to support work related to the research and development of algorithms in the NA-MIC Kit. Algorithms will be driven by the specific needs of the DBPs, but with a preference for generalizable solutions as opposed to algorithms that are only useful in a particular subdomain. Under the development plan for the Algorithms Core (Core 1A), all sites should implement algorithms in ITK and integrate into Slicer3 via the plug-in modules. Core 1A participants are expected to request specific application program interfaces (APIs), data structures, and facilities from Engineering (Core 1B) to support this work.

Core 1B: Engineering

Participants in the Engineering Core are concentrating on developing the NA-MIC Kit as a platform. The platform will provide the libraries and APIs needed by Core 1A to implement their algorithms and the user interfaces needed by Core 2 (DBPs) to make use of these tools. Core 1B participants will consult regularly with the 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 PIs.

Core 2: Driving Biological Projects (DBPs)

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 DBPs are responsible for developing and modifying NA-MIC-Kit applications to meet their specific needs. Thus, third generation DBPs 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 the DBP 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.