Ok, I found one and tried it: opening in a project worked for me. Otherwise QuPath couldn’t find any clues which one it ought to open, and unfortunately the main whole slide image for .scn doesn’t seem to be the first one in the file.
I’ve tried various logic over the years in an effort to open the right one by default… but none totally reliable across all file formats. I recall previously QuPath would open the largest file, which would probably have been more successful here, but was really surprising when applied to a file containing 100 scenes, each representing an individual TMA core - and each with slightly different sizes. It ended up picking one seemingly at random.
Also, previously there was an extra list under the ‘Image’ tab to select different images stored within the same file, but this has been removed because the
ImageServer interface has changed. Currently, the only way to access different images within the same file via Bio-Formats is to add them to a project (apart from things recognised as labels/ancillary images, which are still under the ‘Image’ tab).
The change was made in the service of the ‘fancy’ images mentioned above. It is becoming increasingly important to use projects in QuPath rather than to open images individually to be able to take advantage of all the features. To support that it is becoming easier to create and organize projects.