The Java Image Science Toolkit (JIST) for rapid prototyping and publishing of neuroimaging software

Blake C. Lucas, John A. Bogovic, Aaron Carass, Pierre Louis Bazin, Jerry Ladd Prince, Dzung L. Pham, Bennett A. Landman

Research output: Contribution to journalArticle

Abstract

Non-invasive neuroimaging techniques enable extraordinarily sensitive and specific in vivo study of the structure, functional response and connectivity of biological mechanisms. With these advanced methods comes a heavy reliance on computer-based processing, analysis and interpretation. While the neuroimaging community has produced many excellent academic and commercial tool packages, new tools are often required to interpret new modalities and paradigms. Developing custom tools and ensuring interoperability with existing tools is a significant hurdle. To address these limitations, we present a new framework for algorithm development, that implicitly ensures tool interoperability, generates graphical user interfaces, provides advanced batch processing tools, and, most importantly, requires minimal additional programming or computational overhead. Javabased rapid prototyping with this system is an efficient and practical approach to evaluate new algorithms since the proposed system ensures that rapidly constructed prototypes are actually fully-functional processing modules with support for multiple GUI's, a broad range of file formats, and distributed computation. Herein, we demonstrate MRI image processing with the proposed system for cortical surface extraction in large cross-sectional cohorts, provide a system for fully automated diffusion tensor image analysis, and illustrate how the system can be used as a simulation framework for the development of a new image analysis method. Hie system is released as open source under the Lesser GNU Public License (LGPL) through the Neuroimaging Infoimatics Tools and Resources Clearinghouse (NITRC).

Original languageEnglish (US)
Pages (from-to)5-17
Number of pages13
JournalNeuroinformatics
Volume8
Issue number1
DOIs
StatePublished - Mar 2010

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Neuroimaging
Rapid prototyping
Software
Licensure
Graphical user interfaces
Interoperability
Image analysis
Processing
Magnetic resonance imaging
Tensors
Image processing

Keywords

  • Image processing
  • MRI
  • Parallel processing
  • Pipeline
  • Rapid prototyping

ASJC Scopus subject areas

  • Neuroscience(all)
  • Information Systems
  • Software

Cite this

The Java Image Science Toolkit (JIST) for rapid prototyping and publishing of neuroimaging software. / Lucas, Blake C.; Bogovic, John A.; Carass, Aaron; Bazin, Pierre Louis; Prince, Jerry Ladd; Pham, Dzung L.; Landman, Bennett A.

In: Neuroinformatics, Vol. 8, No. 1, 03.2010, p. 5-17.

Research output: Contribution to journalArticle

Lucas, Blake C. ; Bogovic, John A. ; Carass, Aaron ; Bazin, Pierre Louis ; Prince, Jerry Ladd ; Pham, Dzung L. ; Landman, Bennett A. / The Java Image Science Toolkit (JIST) for rapid prototyping and publishing of neuroimaging software. In: Neuroinformatics. 2010 ; Vol. 8, No. 1. pp. 5-17.
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