Does OMERO natively support 3DHistech images? It seems like this one is not listed as a BioFormat.
MRXS files are a real pain, and are only somewhat supported by OpenSlide.
Have you considered something like this where you use open seadragon?
Hi @samL. Welcome to image.sc!
The short answer is no. OMERO only supports file formats that are implemented in Bio-Formats, and Bio-Formats does not support 3D HISTECH .mrxs files.
If you would like to know the reasoning behind that decision, please see https://blog.openmicroscopy.org/file-formats/community/2016/01/06/format-support/ which (in excerpted form) stated:
3D HISTECH .mrxs is an example of a complex format, the design of which does not make our work any easier. In fact, we can say with some confidence that the 3D HISTECH .mrxs file format is the most complex whole slide imaging file format we have ever encountered.
The OME Consortium and the wider development community have worked steadily since 2002, funded mostly by grants from non-profit charities and public funders, to build tools for the scientific community.
Building readers for proprietary formats has never been funded, and we don’t think it would ever be funded by any grant funding panel…
Perhaps we could crowdsource the funding for file formats but that misses the point—the formats we often lack the resources to support are those which are complex, expensive, difficult, proprietary, closed formats, designed to lock their users into a single, proprietary software application. The community’s resources are finite and should be used for things other than reverse engineering this type of format; work that, if subjected to peer review, would be declined as a waste of community resources.
And that brings us to the more recent blog post https://blog.openmicroscopy.org/community/file-formats/2019/06/25/formats/ (available as a topic here for comment).
We’re very much looking forward to a way past these issues together with the community. But until such time, I hope the forums can help you to find a workaround to this all too common problem.
All the best,