we have an Operetta PerkinElmer CLS system, that we use for different plate types and also whole slide scans. The import of plates works perfectly in Omero, but we are troubling with the whole slide scans. Basically a plate is created and everything saved in the first well:
On the bottom left you can see, that the field positions are properly registered, but for some reason every field position shows the same image. So even if the field ID is changing by clicking on different images, the image looks always the same. I know that bio-formats doesn’t support everything around the Operetta, but does this work as intended? Should I avoid uploading those slide scans into Omero?
With Qupath and Fiji using bio-formats importer it looks a bit different. I can open the related xml-file which then offers all available single field positions as single images correctly, but I am not getting a montage or overview picture offered. I was actually hoping, this kind of data could be analyzed with Qupath, since Fiji will most likely trouble with the size of the data on local computers. Any idea if this is possible at all? Is there maybe some hack to get this work? Or did our users need to change the settings during the image acquisition in Harmony?
Sorry, for mixing the topics a bit, but this Operetta slide scans are a bit of a pain outside of the Harmony software, so I’m happy to get any hints to improve the situation for our users.