As I am Cytomine’s initiator, it’s also hard to give an unbiased opinion, however I tried to somehow distinguish open initiatives (including others you might be interested in) in a (too short) paper last year: https://www.frontiersin.org/articles/10.3389/fmed.2019.00255/full
Please note Cytomine is not relying on OMERO. We have our own databases with extended access rights management with extensive collaborative features through web services and user interface. Latest developments allow multiple users to access the same images within organized and secured projects, annotate them with metadata and semantic information (at the image or ROI level) and build large shareable annotation datasets, compare annotation agreements, execute algorithms directly from the web user interface in a reproducible way through container technology (so any external software can be used incl. imagej, ilastik, cellprofiler, any deep learning libraries,…) on HPC, and review their predictions online, synchronize viewing in real-time over the web, etc.
For slide format reading, Cytomine is using OpenSlide and Bioformats conversion can also be activated to maximize supported formats.
Cytomine is highly interoperable with a Restful API and I think it would be technically feasible to connect Orbit and QuPath for specific desktop analysis using specific algorithms not available in Cytomine (but nobody tried to develop such a bridge as far as I know). For example, the Icy team at Pasteur institute developed a bridge to Cytomine using HTTP requests, so Icy end-users can also analyze their data within Icy and send back results (e.g. annotation predictions) to Cytomine server for sharing.
However, I personally think individual desktop analysis do not fit all use cases, it’s very good to efficiently quantify images and publish papers but I think it might be limited in terms of collaboration.
FYI, Cytomine is also heavily used in education settings with thousands of users, your pathologists might be interested by a common platform for research/education.
To be honest, I think none of these platform will fulfill all your needs. A “day-to-day” solution for specific clinical routine tasks is something else than a software for research projects, therefore extensibility and support/development/maintenance dedicated services might also be something to consider.
As previously suggested, the best way is to test these tools, with the help of people who know how to use them, and analyze how to extend them.
Please feel free to contact us. We can provide a Cytomine online demo account if you are not able to install it locally following our documentation (https://doc.cytomine.org/).