NA-MIC-Kit

• The NA-MIC Kit consists of software that is being made available under the NA-MIC project. This software follows the NIH guidelines for open software development. In this section, we provide information about the components of the NA-MIC kit as well as supporting software tools that are being used by the software developers on the project.

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

• NA-MIC software resources include a number of toolkits, libraries, and applications. Here we provide a brief summary and links to additional information for each NA-MIC software component, as well as a set of processes that will be used for application development using the NA-MIC kit.

Introduction

If you would like to contribute software to NA-MIC, please keep in mind the following guidelines that all our software must follow:

• From the RFA:
  • …NIH does have goals for software dissemination…
  • …software should be freely available …
  • …permit the commercialization of enhanced or customized versions …
  • …include the ability of researchers outside the center and its collaborating projects to modify the source code and to share modifications …
• http://grants1.nih.gov/grants/guide/rfa-files/RFA-RM-04-003.html

• See this presentation with background information and NA-MIC policy presented at the NA-MIC co-sponsored MICCAI 2005 Open Source Software Workshop for more information about how these goals are applied.

• Our conclusion was to standardize on BSD style licenses for the NA-MIC kit.

The NAMIC Kit

See this presentation on the NA-MIC Kit.

The current version of the NAMIC kit consists of the following end-user applications and software toolkits.

Software Applications for Core 3 (DBP) Users

3D Slicer

This a set of tutorials to introduce biomedical scientists to the use of 3D Slicer.

Software Toolkits for Core 1&2 Developers

The following software toolkits are being used to develop software within the NA-MIC community. These should be primarily of interest to the Core 1& 2 participants of NA-MIC.

The Insight Toolkit (ITK)

• This tutorial page points to introductory materials for the ITK software.
• The Insight Journal is an Open Access on-line publication covering the domain of medical image processing.

Software Tools

In addition the following software tools are being used to develop software within the NA-MIC community. These should be primarily of interest to the Core 1& 2 participants of NA-MIC.

Dashboards and BugTrackers

All components of the NA-MIC toolkit have an associated dashboard and bugtracker so that the current state of the toolkit is publicly accessible at all times.

• Dashboards for Components of NA-MIC Kit
• BugTrackers for Components of NA-MIC Kit

Software Engineering Tools improved by NAMIC

• CMake
• CTest
• Dart2

Software Tools Used

• Doxygen
• CableSwig
• Memory Checking (Valgrind and Purify)
• StyleCheck
• SourceNavigator
• Exuberant Tags (CTags)
• Bug Tracking
• CVS (Concurent Versioning System)
• subversion
• Dart
• Version Control
• Python
• TCL/TK
• Java
• C/C++
• OpenGL

Processes

The need for the following processes was identified in early meetings of NA-MIC PIs. Each of these processes are expected to evolve with the project.

• ITK for Matlab Users
• Slicer for Developers
• Mailing lists for NA-MIC Developers
• Tracking NAMIC Contributions to Software Packages
• Test Strategy
• Software_Engineering_Thoughts_and_Links

Documents

The following documents were identified as being useful for development of software and related materials for the NA-MIC community:

• Overview of Software Process
• Style Guide
• Issues Related to using VTK and ITK together