Loading Z-Stacked NDPI Files

[hbilal-md]

Hi Aiosa, i saw a post on image.sc from years ago where someone was talking about needing a NDPI viewer based on openseadragon. Then the follow up comment talks about creating xopat.

Wanted to check in with you to see if this new viewer works with ndpi files directly? Does it support z-stacked NDPI files?

[Aiosa]

Hi, the viewer itself does not concern itself with support for any file formats at all. This is dependent on the server that talks to the viewer. The viewer tries to make it possible to integrate with various services (image and other data) such that it is useable for most use-cases.

So if you have a NDPI-capable image server, and the server either uses a standard high-resolution imaging protocol (DZI, IIIF...) or you implement a new protocol connection, then yes. This server should be able to deal with NDPI. This module implements the logics to connecting to this server.

If you need help with spinning up these services, please let me know.

Regarding the Z-Stack, it is not officially supported on the slide-like behaviour level, but you can still open them. Thanks to its visualization capabilities, the viewer supports timeSeries visuzliation style that takes any child style and groups them with a slider, e.g. using the series with identity will allow you ranging through the Z stack. The issue there is that you are rendering the WSI as a data layer (could be problematic with annotations that measure wrt. base image layer), and you have to provide the data beforehand explicitly, e.g. somehow providing the z-stack in the data session parameter as if each z-stack was an unique file.

To add direct z-stack support for a slide should be rather trivial too, depending on the server and protocol used. Since the recomended viewer supports z-stacks (at least theoretically, never tried myself), all you need to add is a plugin that attaches a slider for the user and sets a target z-stack to read for the linked module. The module would need a small modification too, it would need to add a z query argument to the url, that is a small change I can add.

[Aiosa]

Playing myself with NDPI lately, I am not sure about its full support. All and all, open-source technologies still end up relying on openslide ndpi access implementation under the hood, which is IMHO not mature even today. It fails to read properly slide metadata and reading even top-level slide preview is costly (confirmed myself) when compared to the company proprietary solution. So with our (or mostly other) WSI server there is likely lacking support for optimal slide access, not mentioning z-stack support.

However, xOpat is configurable for use with a WSI service of your choice, so if you manage to use Hamamatsu implementation of the WSI server (which is not free, but exists) and manage to inspect the API and connect (probably issue to get the right token), then indeed this should work.