@smcardle is this where you normally export as BigTIFF? I need to test, but I noticed the OME-TIFF writer is only in certain versions of Zen and I wonder if that would work as well.
@davidnascari There may be other options, but I suspect the easiest way forward, if they are distinct regions anyway, would be to treat them as such by splitting the image into Scenes/files in Zen.
And I can confirm that exporting as OME-TIFF from Zen retains the positions of the different tile regions and can be opened and overlaid on a brightfield image in QuPath. The only downside is that the pixel size is lost and would need to be reapplied using
Oh, and it is a non-pyramidal file, so @smcardle’s recommendation to export via QuPath is still probably the way to go.