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I wish to convert Aperio AFI microscope .svs files from a pathology lab microscope into 3DHistech .mrxs format. Lab ppl have some pipeline X and they asked me to look into the matter.

I can read the SVS files via openslide or openmicroscopy. Conversion to 'regular' pictures (tiff, for instance). I figure out that since openslide can read mrxs, writing this format should be feasible too, but can't find any (free) software to do this. I don't care about any specialties, just need the end result to be readable by Histech readers.

Can anyone help with the conversion? Lacking full software, I could try to code writer if resulting file description is available.

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  • $\begingroup$ Can you please add more context around your actual problem? I'm particularly interested in why writing as .mrxs format is necessary. What do you want to do with it after the conversion? $\endgroup$
    – gringer
    Jun 9, 2023 at 20:40
  • $\begingroup$ It's just that it's unusual for conversion to a non-free format to be necessary, and can be quite a difficult process to get it right. Understanding more about the problem may help to find a better way to go about doing it. $\endgroup$
    – gringer
    Jun 12, 2023 at 10:30
  • $\begingroup$ I've come across this problem before - Aperio SVS files are difficult to wrangle, and are best dealt with using proprietary software. $\endgroup$
    – Ram RS
    Jun 12, 2023 at 13:25
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    $\begingroup$ I had a look at slideio (python module) and this will happily import SVS as an image object, so e.g. matplotlib will work on it .. cool. However there is very little supports for MRXS. I know this because of expert articles such as this, openmicroscopy.org/2016/01/06/format-support.html which is part of openslide. There are saying they wouldn't do it. Certainly the question isn't solvable on this site. Summary, SVS is easy BUT not exporting to MRXS. As @RamRS points out some sort of TissueGnostics purchase looks the only option. Commercial companies keep you locked-in. Upvoted. $\endgroup$
    – M__
    Jun 18, 2023 at 16:35

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If you truly "just need the end result to be readable by Histech readers" the simplest (and maybe even cheapest in the long run) solution might be a paid ($) license for CaseViewer (or whatever their newer viewer is called). I have no idea what that would cost but many of these vendor wsi viewers can read and even write other formats for a price.

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