Support for pyramidal OME-TIFF was only added very recently in libvips – so if you aren’t using the latest version, that may be worth a try (I haven’t used it myself for this purpose, but I’ve seen libvips’ conversion is incredibly fast when it works).
It should (albeit via decompression/recompressing) – see https://qupath.readthedocs.io/en/latest/docs/advanced/command_line.html and in particular check the help from the
convert-ome subcommand at the command line. This has
--pyramid-scale options – it should work regardless of the actual resolution levels in the pyramid, resizing as needed.
If you can go via a QuPath project and Groovy script,
OMEPyramidWriter may give more control: Images registration/alignement, export aligned images
Possibly, but not necessarily… I’ve seen magnifications from different scanners corresponding to very different pixel sizes. It may be worth measuring something that you expect to have a roughly similar size and appears in both images for reassurance (e.g. the diameter of a ‘typical-looking’ nucleus)