XNAT Down Under
Timothy Olsen
I’m just returning home from a visit to the Sydney Imaging Service in Australia. I wanted to take a minute to draw the XNAT community’s attention to the great work this group is doing. They are big fans of XNAT and are taking it to new heights. Thanks to Ryan Sullivan (Director of AIS) and the group for hosting.
The AIS group has gone over and beyond in the goal of building a federation of XNAT’s around the continent of Australia. They’ve done a lot of work around authentication and infrastructure to provide a reliable and consistent environment for hosted XNAT’s in a variety of institutions. And they are pushing the boundaries on processing mechanisms and frameworks.
Here are just a few of the things they are working on which may be of interest to you in your XNAT journey.
https://bitbucket.org/xnatx/openid-auth-plugin
Several years ago, the Sydney group invested in building an OpenID plugin that has become a staple for many in the XNAT community. If you aren’t using it, I’d highly suggest reviewing it and seeing if it could integrate with your institution's authentication framework.
The group has pioneered an infrastructure framework for XNAT (and other resources) that should be useful throughout the wider community. They are building on k8s, which is becoming more and more prominent across institutions for its reliability and consistency. In particular, check out their resources on managing XNAT in K8s: AIS XNAT | Australian Imaging Service. But their general framework (which can also host RedCap and CTP) is worth digging into.
Jupyter Workbench workflows (SciGet i.e. Neurodesk)
The AIS group has invested in getting Neurodesk and SciGet working on their XNAT infrastructure. They are to the point of having a fully sandboxed virtual linux environment accessible IN their XNAT with the data loaded and ready to go. It’s really cool stuff. There first generation of work was around Neurodesk; https://neurodesk.org/. But, they’ve been rebranding it to SCIGET. Check it out!
PYDRA
Tom Close, an old friend of XNAT, has been investing years into a project that I expect will be very effective for the wider community. Its still in the works and being finalized, but it’s really cool stuff. “Pydra is a lightweight dataflow engine written in Python. Although designed to succeed Nipype in order to address the needs of the neuroimaging community, Pydra can be used for analytics in any scientific domain” Workflow engine: https://nipype.github.io/pydra/ App code: https://arcanaframework.github.io/pydra2app/index.html We’ll arrange a demo to the XNAT community soon, but in the meantime, have a look and give Tom any feedback you can manage.
Founding GIDE
While I was in town, they invited me to join the Founding GIDE annual meeting. This is a great group that is promoting the creation of a global network of imaging repositories. If you haven’t heard of it, check it out. It reminds me a lot of the dreams we had in the early days of the XNAT project. It’s great to see researchers making the push to get there. foundingGIDE - Founding a Global Image Data Ecosystem - FoundingGIDE Their next meeting is May the 4th in Germany, if you are interested, Ryan may try to get a group of XNAT’ers there.
We’ll arrange for the group to do some recorded demos for the community soon. But, in the meantime, dig in.
Ryan Sullivan, please post more information to the discussion group as you have more to share.
Happy XNAT’ing!
Tim
Timothy R Olsen
Founder, President
Tour of the preclinical imaging facility in Sydney.
A PET/CT for mice.
Fang Xu has been running XNAT's in Sydney for years.
Saori Tanaka Phd, they use XNAT in her research in Japan. We didn’t know there were any XNAT’s in Japan. There ARE!
Dario Livio Longo Phd (Torino Italy), Ryan Sullivan Phd (Sydney AUS), Tom Close Phd (Sydney AUS) at lunch at the Founding GIDE conference
Timothy R Olsen
Founder, President