Nanozoomer annotation coordinate system to openslide pixels

Ali Hassan Raza ahraza at
Sat Jul 2 22:23:06 EDT 2022

Hello Benjamin,

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 rigshospital in Copenhagen, and they use a scanner from hamamatsu. The WSI they have provided are in the format of NDPI alongside the annotation the pathologist have done which are in NDPA format.

I want to segmentate the areas (create a mask) where the pathologist have done annotations, so that I can make some 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 your debat. I am stuck and would be very thankful if you could help me in my need and explain how you managed to convert these coordinates. I am coding in python using jupyter notebook. 

Kind Regards
Ali Hassan Raza
Roskilde University

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