Currently I work with multiplex fluorescence .mrxs datasets, unfortunately (the equipment itself is ok, but this data format require a lot of workaround).
I plan to do my main data analysis in QuPath, and because of this I tend to experiment with bioformats2raw and raw2ometiff. The converters themselves ran without any errors, but at the end of the process i lose my z (axial) slices and get a max projection image instead. Additionally, a few of my channels switch names, too (I currently use 6 chanels).
I really newby in this field, but i didn’t find a solution neither in the -helper menu of commands nor in any topics of issues. I use MacOs and installed both converter by conda.
I would appreciate any suggestions. Many thx