MRXS files in Qupath

Hello,
I am using a scanner that provided MRXS files with 4 IF channels,
and the Qupath has a problem to open all the 4 channels.
how can I fix it?
Thank you,
Shimrit

Unfortunately mrxs is a proprietary file format and for that reason QuPath cannot fully support it. There is more information and explanation at https://qupath.readthedocs.io/en/latest/docs/intro/formats.html#mrxs-3d-histech

Changing this would require the cooperation of the company behind the file format. In the end it is their decision how open they want to be, and if they want to make it possible for their customers to work with their data in open software or not.

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You may want to try exporting it as another format.


I don’t have any recent experience with CaseViewer, but it looks like they now support SVS format.

As far as I know, the SVS export doesn’t solve the problem - although would be happy to find out that’s not true :slight_smile:

(In the end, SVS is TIFF of some kind, and there is a lot of variation in how the data might be stored inside the TIFF…)

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I was hoping it would fix the 4 channel RGB problem, if not the JPEGXR problem. But I haven’t tested it. There’s no way I’m installing CaseViewer again.

Hi Pete,

There was a recent workaround for this by glencore

https://www.glencoesoftware.com/blog/2019/12/09/converting-whole-slide-images-to-OME-TIFF.html

Can this be used in QuPath somehow ?
Many people would love to use QuPath for these files.

Thanks
Ofra

@Ofra_Golani: The workflow that we outlined on the blog post, which is via conversion to pyramidal OME-TIFF, is very much compatible with QuPath. Via Bio-Formats, QuPath and OMERO support OME-TIFF natively.

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Thanks Chris,

Does it mean that I must convert the file to ome.tif as described in the blog, before opening it in QuPath? or can I somehow do the conversion within QuPath ?

Is there any intention to implement this 2 steps conversion into bioformats ?

Ofra

Hi @Ofra_Golani there isn’t a way to read the .mrxs images directly into QuPath - using the workflow from Glencoe Software, the files would need to be converted.

I’d defer to @chris-allan if there’s a better way QuPath could/should support this workflow.

In the end, I very much hope that customers are making clear to the companies creating these formats that open source compatibility is important to them.

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@Ofra_Golani: Yes, you must convert the MRXS file into an OME-TIFF as described in the blog and then open the resulting OME-TIFF in QuPath. We could certainly work with @Pete to integrate the conversion tools into QuPath but that is not possible currently.

At the moment, no, there is no intention to implement the two step workflow in Bio-Formats.