Relative Roles Core1a Core 1b Core2

Introduction

In 2007, NA-MIC DBP funding moved from the first generation of DBP to a second generation. This is an opportunity to rethink the roles and functions of the Algorithm, Engineering, and DBP cores.

The RFA says the following (excerpts):

• Core functions:

1. conducting core research in relevant science, such as algorithm creation and optimization
2. developing and deploying tools designed to solve particular biomedical problems
3. establishing Driving Biological Projects (DBP) to allow experimental biomedical and behavioral researchers to interact with and drive computational research in the NIH NCBC

The RFA for the second generation of DBP's contained the following language defining the role of NA-MIC funding in their enterprises:

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

The Introduction for the NA-MIC kit contains the following definition:

• 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 all of this background and on conclusions with the experience from the first three years of operation the following guidelines are emerging for the role of the each of the 3 main cores of NA-MIC.

Overall objective

Developing the NA-MIC kit into a full-fledged environment for Medical Image Computing research. This requires a set of general purpose tools adaptable to a range applications. All the NA-MIC participants will use NA-MIC funding exclusively for this overall goal.

Core 1: Algorithms

NA-MIC funding should be used for work inside the NA-MIC kit or to optimize algorithms for the NA-MIC kit. Algorithms are must be driven by the specific needs of the DBPs but with a preference for general solutions as opposed to algorithms that are only useful in a subdomain. A successful algorithm becomes available as a supported tool, implemented in ITK, with a Slicer3 user-interface.

Core 2: Engineering

Participants in this core are concentrating on developing the NA-MIC kit as an infrastructure. The infrastructure must provide the libraries needed by Core 1 to implement their algorithms and the interfaces needed by Core 3 to make use of the tools.

Core 3: DBP's

The second generation DBP's use the NA-MIC funding to hire a Slicer engineer who will help to use the tools developed by the algorithm core to perform biomedical research. Core 3 researchers serve as representatives of their fields and should make algorithm and tool requests that serve not just their current research needs, but will also benefit the larger community of users.

Case studies

• Georgia tech: DLPFC parcelation tool
  • Both algorithm and the implementation done by students at Georgia Tech
• MIT: EM segmenter
  • Algorithm research partially predates NA-MIC
  • Part of the tool creation was outsourced to kitware, using MIT NA-MIC funding
  • Algorithm has multiple applications (MR Neuro, CT Torso, Mircoscopy...) all available in a clean and documented user interface.