XNAT-OHIF viewer plugin 3.7.0: the digital pathology release

[Simon Doran]

Dear All,

  I wanted to give a big shout out to my colleague Mo Al S'ad for an outstanding piece of work in putting together the latest release (3.7.0, available at the usual download.xnat.org site) of the XNAT-OHIF viewer, the first to support digital pathology whole-slide imaging (WSI) data. The release notes describe factually what has been created but don't adequately reflect what a significant achievement this is.

  For the first time, the DICOM SM modality is now a "first class" citizen in XNAT. Consider this list of experiments from an XNAT subject report page from the workup phase of one of our local projects.

  Clicking on View Images brings all the DICOM data into the viewer, where the digital path data can be accessed from the left hand series browser and dragged into viewports just like any radiology modality:

When you use the viewer, you will notice that the available tools along the top and the available right-hand sidebar items update to provide only what is relevant for the modality in the viewport with mouse focus. A new info panel has been created with the slide label and the set of available channels, which can all be turned on and off separately. In the example below, three different zoom levels and three different combinations of displayed channels are illustrated. Work is ongoing to port functionality such as creation of ROIs into the digital pathology context.

A thumbnail slide overview panel at the bottom left allows easy navigation, and panning and zooming are rapid even at high magnifications. To achieve the excellent performance has taken a lot of hard work and Mo has completely rewritten the DICOMweb backend for XNAT. Much of the related architectural work is also laying the foundations for our next release, coming soon, which will be another large step forward, as we transition the XNAT-OHIF viewer to the latest Cornerstone3D libraries and an entirely new viewing experience. But more of this later in the autumn...

So, practically, how do you get microscopy data into XNAT?

Some vendors make it easy to write DICOM data directly from their platforms. For others, it is more difficult and you may need to "roll your own". Our team is not in a position to take on responsibility for supporting this process, but we can provide some useful pointers as to what has proved useful. You may like to take a look at:

• the Imaging Data Commons (IDC) data conversation process described here;
• the wsidicomizer project;
• Google Cloud Platform's wsi2dicom tool.

Once you have  your data in DICOM form, it's then straightforward to send this to XNAT's standard DICOM receiver, for example with DicomBrowser, or to use XNAT's compressed uploader, and XNAT will create a new SM Session for you. If this is the first microscopy data you have on the platform, you might also have to enable the SM Session data type.

Finally, it's worth pointing out that, if you can afford the space to double-store your data, you might be wise to use XNAT's "Manage Files" functionality to store a copy of the original vendor's native-format WSI file in case there are data that have not been fully extracted by the current WSI-TO-DICOM conversion tools.

If you need any help, please get in touch and we will do our best to get you started.

Happy viewing!

Best wishes,

Simon

[Simon Doran]

Better version of the third figure: