How to access MIRAX files's image orientation, position and pixel spacing.

[DanielaSchacherer]

Slide format

MRXS

Issue details

Hello together,

I am currently converting MIRAX WSI slides that go along with annotations using wsidicomizer (see imi-bigpicture/wsidicomizer#126)

I have bounding boxes that were generated with QuPath using the original MIRAX slides (which means they refer to MIRAX image coordinates: 0,0 at the top-left corner of a pixel). I was thinking the most clean and reproducible way to transfer those annotations to the converted DICOM slides is to use highdicom's ImageToImageTransformer. For that,
I need to extract the orientation (for DICOM ImageOrientationSlide), position (for DICOM TotalPixelMatrixOriginSequence), and pixel spacing (for DICOM SharedFunctionalGroupsSequence[0].PixelMeasuresSequence[0].PixelSpacing).

Since wsidiomizer uses openslide-python for handling MIRAX files, I wondered if you can you tell me how to access orientation, position and pixel spacing from the MIRAX slide.

Best regards,
Daniela

[bgilbert]

Everything OpenSlide knows about MIRAX slide metadata is included in the slide properties. You can get pixel spacing from openslide.mpp-x and openslide.mpp-y. I'm not aware that the MIRAX metadata encodes the other information you're looking for, but you can look through the properties and see if you find anything useful.

[DanielaSchacherer]

@bgilbert thank you very much for the quick answer. I know about slide properties and that it contains pixel spacing(s). I couldn't find anything about the image orientation and position and was thus hoping that you'd know more.