Thanks Tristan. I've opened a ticket on our issue tracking system for the lookup table issue:
http://trac.openmicroscopy.org/ome/ticket/12836
and you have been CC'd.
Does the file uploaded to QA 10991 also illustrate points (1) - (4)? Please note that we don't have other software that can open .msr files, we don't have specifications, and for most sample .msr files we don't have a description of the expected metadata, so we're a little more blind than usual for this particular format. Anything you can provide in terms of files that show these problems and screenshots of the expected display and/or metadata would be greatly appreciated, and would help us to resolve these problems more quickly.
Regards,
-Melissa