Import annotations from .mrxs files

[cklat]

Hi there,

I wanted to ask if there's an option in QuPath to import annotations made in the with .mrxs files coming from a 3D-Histech Scanner. I got several .mrxs files that go with folders in which a bunch of .dat files are located. I'm not sure in which way the files for one whole slide image is structered but I believe the annotation data must be included in one of the files, either the .mrxs file or the .dat files.

Thanks for your help!

[petebankhead]

I didn't actually know .mrxs files could contain annotations...

The first post here contains the teasing phrase 'pure xml with pretty obvious content', although it's not clear to me how easy it is to know which .dat file contains the annotations in each case.

@DanaCase created a really useful script to parse Aperio annotations at #61 (comment)

Creating a parser that can handle annotations in a variety of formats could be an extremely useful contribution (and 'fun' student project?)... I'm afraid it's not something I am likely to get a chance to work on myself any time soon, but I can help with the QuPath side (i.e. converting coordinates into ROIs and objects that QuPath can display).

I'll flag this as 'help wanted'...

[erexhepa]

.mrxs files do contain annotations created with viewer/management plaftorm from 3DHistech. They are contained in the folder corresponding to the digital slide. You have to parse the .dat files and look the last 3 files (from the numerical index) for an XML formated text at the beginning of the file. There isn't much documentation about their file format to be able to automate the interpretation of the annotations (i.e. which one is the file with the annotations 2nd/3rd as it depends on the version of scanner and software controller).

Sometime you see within the annotations file some annotations that are not displayed in the viewer from 3DHistech (i.e. deleted annotations). What I would recommend is to name the annotations (when you crate them) with labels you define yourself so that you know what to look for when parsing the xlm file.

Let me know if you have more questions.

[cklat]

Thanks for the clarification!

It wasn't my intention to point out that the .mrxs itself contains the annotation meta data but that it should be somewhere included in one of the files that go together with the .mrxs.
But it seems @erexhepa is on the right track here as I was able to identify some xml text in one of the indexed .dat files. That definitely helps a lot at this point, thanks a lot!

[petebankhead]

Closing this because of lack of activity, and because http://forum.image.sc/tags/qupath is now the best place for further discussion.

v0.2.0-m3 also includes some initial support for GeoJSON - so importing annotations from other formats may in the future be separated from QuPath as a 'convert to GeoJSON' task.