Support for .mrxs files + best walkarounds?

Hello everyone.

I recognize that this topic had been discussed multiple times before, but just wanted to know if there were any recent changes.

As far as I recognize, QuPath utilizes two libraries - OpenSlides and Bio-formats - to read whole-slide images, and these libraries do not support MRXS file format So MRXS files cannot be opened directly in QuPath.

Are there any possibilities for MRXS file format to be supported by QuPath in the near future? (this I doubt)
If not, what is the best practice to work with MRXS files with QuPath? Would converting MRXS files into OME-TIFF files be the best solution? If then, would it be possible to write a script that automatically converts MRXS files to compatible file format when loaded in QuPath?

Thank you very much!

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Hey Seung,

openslide supports .mrxs format and I’m able to open such files in Qupath. But I also had problems opening .mrxs files with openslide/qupath in the past and fixed this by opening these specific files in the 3D Histech Slide Converter and exporting them from .mrxs to .mrxs. I hope this solves your issue.


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Usually this is due to encoding with JPEGXR.

Some of the newer MRXS formats seem to have more in depth issues, and require one of the pipelines previously discussed.

If you’re comfortable with command line scripting, you can try the method described here:

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