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XNAT

Extensible Imaging Archive Toolkit. Archiving, viewing and analysing clinical imaging data.

x-ray images
Chevron Down Icon of a chevron pointing down About

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 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 (see Fair use and Freemium Pricing)
  • Secure deployment by professional hosting party
  • High-quality user support via Health-RI Servicedesk

Chevron Down Icon of a chevron pointing down Getting Started

Getting Started

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

  1. 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
  2. Login to the Health-RI Self Service Desk with your account information .
  3. 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.

Chevron Down Icon of a chevron pointing down Support

Support

A short introduction to using XNAT

Setting up of studies and support of users in Health-RI XNAT is carried out by the Health-RI service desk.

Large user and active development community

XNAT and CTP are supported by large communities and/or organizations guaranteeing their continued development. As open-source applications: users can review and enhance the source code which will become available for the entire community.

Users can ask questions, submit suggestions for new features, and report issues in user forums or directly with developing organizations. XNAT is maintained by the Washington University School of Medicine and CTP by the Radiological Society of North America (RSNA).

Training

There is no formal training for Health-RI XNAT at the moment.
Please monitor the Health-RI training portfolio
 for available training.

For questions regarding the XNAT training program and to request a temporary training environment contact the Health-RI servicedesk.

Chevron Down Icon of a chevron pointing down Further information

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.

XNAT Freemium and FAIR use 

Research projects that were initiated in the Netherlands can make use of Health-RI XNAT.  

Unless otherwise specified here, the regular fair use policy and freemium pricing for Health-RI Services also apply to XNAT. See 'Fair Use policy and Freemium pricing'

A fair-use policy applies to Health-RI XNAT (see also Fair use and Freemium Pricing

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 attitude.

In 2020, research projects can use the TraIT XNAT server free of charge, however a fair-use policy applies: Projects having high demands with respect to computing capacity, disk space, network bandwidth or consultancy should fund this from their own project budget. More specifications on what is Freemium will be included in this page soon.

The pricing model for 2020 (excluding BTW) can be found on the TraIT project website. Please contact the Health-RI Service Desk for more information on the 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.

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

Datatypes Clinical Imaging Data
Research Process Data generation
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