Conference proceeding
Extending the XNAT archive tool for image and analysis management in ophthalmology research
Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol.8674, pp.86740M-86740M-14
03/29/2013
DOI: 10.1117/12.2007966
Abstract
In ophthalmology, various modalities and tests are utilized to obtain vital information on the eye’s structure and function. For example, optical coherence tomography (OCT) is utilized to diagnose, screen, and aid treatment of eye diseases like macular degeneration or glaucoma. Such data are complemented by photographic retinal fundus images and functional tests on the visual field. DICOM isn’t widely used yet, though, and frequently images are encoded in proprietary formats. The eXtensible Neuroimaging Archive Tool (XNAT) is an open-source NIH-funded framework for research PACS and is in use at the University of Iowa for neurological research applications. Its use for ophthalmology was hence desirable but posed new challenges due to data types thus far not considered and the lack of standardized formats. We developed custom tools for data types not natively recognized by XNAT itself using XNAT’s low-level REST API. Vendor-provided tools can be included as necessary to convert proprietary data sets into valid DICOM. Clients can access the data in a standardized format while still retaining the original format if needed by specific analysis tools. With respective project-specific permissions, results like segmentations or quantitative evaluations can be stored as additional resources to previously uploaded datasets. Applications can use our abstract-level Python or C/C++ API to communicate with the XNAT instance. This paper describes concepts and details of the designed upload script templates, which can be customized to the needs of specific projects, and the novel client-side communication API which allows integration into new or existing research applications.
Details
- Title: Subtitle
- Extending the XNAT archive tool for image and analysis management in ophthalmology research
- Creators
- Andreas Wahle - Iowa Institute for Biomedical Imaging, The Univ. of Iowa (United States)Kyungmoo Lee - Iowa Institute for Biomedical Imaging, The Univ. of Iowa (United States)Adam T Harding - The Univ. of Iowa (United States)Mona K Garvin - Iowa Institute for Biomedical Imaging, The Univ. of Iowa (United States)Meindert Niemeijer - Iowa Institute for Biomedical Imaging, The Univ. of Iowa (United States)Milan Sonka - Iowa Institute for Biomedical Imaging, The Univ. of Iowa (United States)Michael D Abràmoff - Iowa Institute for Biomedical Imaging, The Univ. of Iowa (United States)
- Contributors
- Maria Y Law (Editor) - Hong Kong Sanatorium and Hospital (Hong Kong, China)William W Boonn (Editor) - Univ. of Pennsylvania Health System (United States)
- Resource Type
- Conference proceeding
- Publication Details
- Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol.8674, pp.86740M-86740M-14
- DOI
- 10.1117/12.2007966
- ISSN
- 1605-7422
- Publisher
- SPIE
- Language
- English
- Date published
- 03/29/2013
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Radiation Oncology; Fraternal Order of Eagles Diabetes Research Center; Injury Prevention Research Center; Ophthalmology and Visual Sciences
- Record Identifier
- 9984047608602771
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