Can bioformats2raw convert z-slices from .mrxs data?

Hello everyone!

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

Balint Fazekas

Hello, Balint. Unfortunately MRXS support in bioformats2raw does not currently include support for Z sections. Please see:

At the moment no work on this is scheduled. If you are not able to contribute support for this yourself you can contact Glencoe Software to sponsor support:

1 Like

Hi Chris!

Thank you very much for your reply!

I will upload this topic if i could do anything by myself.

TY again,