Health-RI XNAT Medical Imaging Service
Extensible Imaging Archive Toolkit. Archiving, viewing and analysing clinical imaging data.
About
XNAT is an open source imaging informatics platform. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data.
Health-RI hosts and supports this service for research projects aiming at archiving, viewing and analysing clinical imaging data.
Features
XNAT enables access to data via
- Manual upload and download via a website
- With the DICOM® (Digital Imaging and Communications in Medicine) protocol
- an application programming interface (API).
XNAT stores images along with image-derived information such as annotations and processed versions of the images. It is therefore recommended for large studies that require automated image analysis by advanced, technically oriented researchers.
Even though XNAT provides image querying and viewing capabilities, Image data in XNAT can also be queried and retrieved by many viewers through the XNAT Gateway. These include popular viewers such as Osirix and 3D Slicer. See more on image viewing in XNAT
Advantages and conditions of using Health-RI XNAT
- Only the Principal Investigator (PI) has data control
- Links to other data storage and analysis tools within the Health-RI platform, enabling you to directly open the specific patient images in XNAT from within the other tool. This allows researchers to integrate and analyse case-report data, imaging data, experimental data and bio banking information.
- Multi Center Access to data. The XNAT environment is accessible via the internet, enabling sharing of data for multi-center studies.
- Can be implemented in an ecosystem of research tools like the BBMRI image analysis platform.
- A fair-use policy applies, associated with a terms of use and pricing model.
- Secure deployment by professional hosting party.
- High-quality user support via Health-RI Servicedesk.
Getting Started
Pricing model and conditions
Research projects that were initiated in the Netherlands can make use of Health-RI XNAT.
A fair-use policy applies to the use of XNAT, associated with a terms and conditions and pricing model.
Each XNAT study should make sure not to perform activities that could potentially be disruptive for the proper operation of the XNAT service in general (fair use policy). Please contact Health-RI before performing activities which could cause excessive load disruptive for other users. These include: large data uploads, use of the REST-API, automated data entry scripts, a.o.
Request user and collection account
To start using XNAT for your study, images need to be uploaded to a new project.
File a request with the Health-RI service desk
- Please mail servicedesk@health-ri.nl and request a user account for the Health-RI Self Service Desk, explaining you intend to use XNAT for your research project
- Login to the Health-RI Self Service Desk with your account information .
- Fill out and submit the form: 'XNAT New Collection Request' for XNAT. This request includes an account for the person who will manage the XNAT Collection on the Health-RI server and will act as Collection Administrator by default. This collection administrator also has a coordinating role to set-up the study.
The preparation for submitting images to XNAT can be a lengthy iterative process, partly because of the pseudonymisation process. Health-RI uses CTP. We strongly advise to follow the instructions on the step by step guide to get your study up and running in Health-RI XNAT. For questions or advice, please contact the Health-RI Servicedesk.
Support
A brief introduction to using XNAT.
Setting up studies and user support in Health-RI XNAT is carried out by the Health-RI service desk.
Health-RI supports users in the Health-RI XNAT environment. Support is provided for specific questions/problems related to the XNAT software, but the support model assumes a do-it-yourself approach.
Large user and active development community
XNAT and CTP are supported by large communities and/or organisations that guarantee their continuous development. As open-source applications, users can view and improve the source code, which becomes available to the whole community.
Users can ask questions, suggest new features and report problems in user forums or directly to developing organisations. XNAT is maintained by the Washington University School of Medicine and CTP by the Radiological Society of North America (RSNA).
Training
There is currently no formal training available for Health-RI XNAT.
Questions
For questions about the XNAT training programme and to request a temporary training environment, please contact the Health-RI service desk.
Further information
Security and Privacy
Health-RI security measures
Health-RI offers a tailor-made Technical and organizational quality system to manage legal, customer and ICT-security requirements.
Health-RI uses standardized procedures (SOPs) for creating new user accounts in order to comply to the data owner’s data access policies and to prevent unauthorized access to study data.
Secure deployment by professional hosting party
The Health-RI XNAT environment is hosted by Vancis and meets the ISO 27001 standard for information security management. The network communication with the XNAT web-application (incl. the upload process) is secured via the HTTPS protocol, meaning that hospitals do not have to open ports on their firewall (assuming the basic HTTPS port is open to the outside world).
Our certificate guarantees that the Health-RI XNAT user is really communicating with the Health-RI XNAT environment.
Our infrastructure architecture has been optimized for data security. The XNAT database is backed up every night and every other year we perform a disaster recovery test.
Health-RI takes security seriously at the application level. It works with controlled access through user accounts and authorization at the level of study and role. XNAT offers similar authorization options.
For each project in XNAT, the data controller, generally the principal investigator of the research project, or an appointed delegate, decides who gets access to the study and indicates the role/authorization that should be applied to the user account. The institute or investigator that supplies the data to Health-RI remains the owner of the data and access to the data is controlled by the owner. In order to comply to privacy regulations, it is only allowed to store anonymized or pseudonymized data on the Health-RI XNAT server.
The visibility of a project/collection can be set as:
- Public: all project data visible to outside world.
- Protected: project description visible to other users, but image (derived) data not. Users can request access
- Private: As a default, the project is only visible to logged in project members
The data controller can change this any moment.
For more information, please see: XNAT User roles and Permissions.
Security at transport level, especially with regards to data collection/ingestion and data consumption, is covered by standard ciphering protocols for encrypted communication over the Internet.
Current version and release notes
1.7.5 (release notes)
XNAT was originally developed as Extensible Neuroimaging Archive Toolkit at Washington University in the Buckner Lab, which is now located at Harvard University.
For information on the organization behind XNAT visit this page.
For technical background information visit this page.
References
XNAT:
Marcus DS, Olsen T, Ramaratnam M, Buckner RL: The Extensible Neuroimaging Archive Toolkit (XNAT): An informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics. 2007, 5 (1): 11-34
XNAT.bmia.nl:
Klein S, Vast E, van Soest J, Dekker A, Koek M, Niessen W: XNAT imaging platform for BioMedBridges and CTMM TraIT. Journal of Clinical Bioinformatics. 2015, 5(Suppl 1): S18
About BMIA.nl (in Dutch):
Dekker A, van Soest J, Klein S, Hoekstra R, Groot P, Vast E, Huguet J, Niessen WJ, Boiten J-W, van der Lugt A: BMIA – nationaal biomedisch imaging archief voor onderzoek. MemoRad. 2015, 2: 7-10
This may also interest you 
Erasmus MC Imaging Office data storage and management |
