Actual resolution of Mirax WSIs in QuPath

Usage & Issues
#1

Hi all,

I was wondering if QuPath is doing some sort of cropping/limitation to the actual relevant image section for mirax file format.

I have some mirax WSIs that do have a size of 272.000 x 294.000 according to OpenSlide and the 3DHistech SDK. QuPath opens these slide files using an OpenSlide-server instance but is only displaying a cropped region of 83.000 x 116.000 (what is more or less the ROI of the tissue). I am creating some annotations manually that I want to process afterwards. But the coordinates of these annotations are useless since they are not global.

Can anyone explain how this works in QuPath and if there is a way to retrieve the global coordinates? Any other workaround?

With other file formats like ndpi or svs I don’t face this issue.

Thanks a lot in advance.
Regards

#2

Hi @michael_ef, QuPath v0.2 applies the bounding box; the coordinates are available in OpenSlide if you need to correct for this elsewhere: List of Known Properties

If you want to access them from QuPath, the following script should work

def server = getCurrentServer()
print([server.boundsX, server.boundsY, server.boundsWidth, server.boundsHeight])

but it’s a bit of a hack that might potentially break in future versions (since it is sneakily accessing private variables).

#3

Thanks a lot @petebankhead. Is there also a way to deactivate the bounding box?

#4

I’m afraid not. The bounding box wasn’t used in QuPath v0.1.2, but this could cause trouble and inconsistency with some formats (e.g. with .scn I believe Bio-Formats would read the image with the cropping applied automatically) and also plays havoc with image statistics because of the large numbers of uninformative pixels.

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