Need help urgent

[Ali Hassan Raza]

Hello Openslide members,

I am desperately in need of help. My name is Ali, and I am a masters level student in computer science at roskilde university in Denmark. I am writing my masters thesis in cardiac biopsy using a deep learning approach. The dataset I am working with is from the hospital rigshospital in Copenhagen, and they use a scanner from hamamatsu which saves the WSI in the format of NDPI alongside the annotation the pathologist have done which are in NDPI.NDPA format.

I want to segmentate the areas (create a mask) where the pathologist have done annotations, so that I can make some deep learning models which can learn from the masks, and thereby test them on some data to see how well the model performs. I did som research on the internet and could not find anything about how to convert these coordinates, until I came across some posts where people have suggested that openslide plugin may be useful.

The problem I have is that the annotations the pathologist have done on the ndpi wsi have negative x and y coordinates, which means that the coordinates system in ndpi format has 0,0 in the center of the slide (I guess) and not the top left corner as normal images. I am stuck at the moment, and don’t know how to deal with the ndpi.ndpa annotations, and would be very thankful if you could help me. I am coding in python using jupyter notebook.

Kind Regards
Ali Hassan Raza
Roskilde University
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