title: BrainImageJ: a Java-based framework for interoperability in neuroscience, with specific application to neuroimaging.
abstract: The Human Brain Project consortium continues to struggle with effective sharing of tools. To facilitate reuse of its tools, the Stanford Psychiatry Neuroimaging Laboratory (SPNL) has developed BrainImageJ, a new software framework in Java. The framework consists of two components-a set of four programming interfaces and an application front end. The four interfaces define extension pathways for new data models, file loaders and savers, algorithms, and visualization tools. Any Java class that implements one of these interfaces qualifies as a BrainImageJ plug-in-a self-contained tool. After automatically detecting and incorporating new plug-ins, the application front end transparently generates graphical user interfaces that provide access to plug-in functionality. New plug-ins interoperate with existing ones immediately through the front end. BrainImageJ is used at the Stanford Psychiatry Neuroimaging Laboratory to develop image-analysis algorithms and three-dimensional visualization tools. It is the goal of our development group that, once the framework is placed in the public domain, it will serve as an interlaboratory platform for designing, distributing, and using interoperable tools.
authors.affiliation: Stanford University, Stanford, California 94305-5719, USA.
authors.forename: Y R
authors.initials: YR
authors.lastname: Ng
authors.forename: S
authors.initials: S
authors.lastname: Shiffman
authors.forename: T J
authors.initials: TJ
authors.lastname: Brosnan
authors.forename: J M
authors.initials: JM
authors.lastname: Links
authors.forename: L S
authors.initials: LS
authors.lastname: Beach
authors.forename: N S
authors.initials: NS
authors.lastname: Judge
authors.forename: Y
authors.initials: Y
authors.lastname: Xu
authors.forename: U V
authors.initials: UV
authors.lastname: Kelkar
authors.forename: A L
authors.initials: AL
authors.lastname: Reiss
mesh_terms: D000465:Algorithms; D000716:Anatomy, Artistic; D019412:Anatomy, Cross-Sectional; D001921:Brain / Q000033:anatomy & histology*; D006801:Humans; D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional; D008032:Limbic System / Q000033:anatomy & histology; D008488:Medical Illustration; D009445:Neuroanatomy / Q000379:methods; D011381:Programming Languages; D012984:Software; D012985:Software Design; D018511:Systems Integration; D014584:User-Computer Interface