The XNAT Ecosystem
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1
Washington University in St. Louis, United States
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2
Deck5 Consulting, United States
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3
Integrity, United States
The XNAT imaging informatics platform is widely used to manage a variety of neuroimaging research, from internal research programs to large-scale data sharing initiatives. While XNAT has been open source since its inception and developers from around the world have contributed to its features, the number of contributions has been limited due to the scale and complexity of the XNAT code base. However, with the inclusion in recent releases of XNAT of an open application programming interface (API) based on the REST web services model, many more developers are developing tools that interact with XNAT through the API without needing to learn XNAT's internal code. Examples include pyXNAT, a python library for exchanging data with XNAT; Connectome Workbench, a visualization and analysis platform for structural and functional MRI data; and 3D Slicer, an advanced medical image visualization suite; and LONI Pipeline, a GUI-based application for executing and managing automated processing streams. A variety of additional tools are currently in development. The most recent version of XNAT includes a plugin architecture that enables developers to build new capabilities directly in XNAT with minimal interfacing in the core code. Modules can include visual components as well java code and extensions to the XNAT REST API. As an example, our lab has produced a module that enables users to pull XNAT metadata into iCal calendar feeds. These feeds can be used to assist study monitoring by integrating views of data in scheduling systems (e.g. Google calendar) by the date and time of acquisition in an integrated view with scheduling. To assist in dissemination of XNAT related software, we have developed a sharing resource called XNAT Marketplace (https://marketplace.xnat.org) where developers can contribute and share modules, scripts, and other tools along with documentation. XNAT Marketplace interface and features were designed following patterns established by similar software dissemination sites such as Firefox Add-ons (https://addons.mozilla.org/en-US/firefox/extensions/). Marketplace includes categories, featured plug-ins, a search interface, a tool upload interface, and tool versioning. Together, the API, XNAT plugins, external tools that interact with XNAT, and the XNAT marketplace make up an ecosystem of informatics tools and applications that enable new capabilities in neuroimaging research.
Acknowledgements
This work was supported by the Biomedical Informatics Research Network (BIRN) (U24 GM104203), the National Alliance for Medical Image Computing (NAMIC) (U54 EB005149), and XNAT (R01 EB009352).
Keywords:
XNAT,
data sharing,
open source,
plugins,
database
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Poster
Topic:
Neuroimaging
Citation:
Marcus
D,
Herrick
R,
Olsen
T,
Horton
W and
Sheu
A
(2013). The XNAT Ecosystem.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00102
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Received:
29 Apr 2013;
Published Online:
11 Jul 2013.
*
Correspondence:
Dr. Daniel Marcus, Washington University in St. Louis, St. Louis, United States, dmarcus@wustl.edu