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Hi Ali,
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<div class="">Is there any example data we can try to help ? </div>
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<div class="">Yu Zhao<br class="">
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<div class="">On Jul 6, 2022, at 1:18 PM, Ali Hassan Raza via openslide-users <<a href="mailto:openslide-users@lists.andrew.cmu.edu" class="">openslide-users@lists.andrew.cmu.edu</a>> wrote:</div>
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<span class="" style="caret-color: rgb(0, 0, 0);">Hello Openslide members,</span><br class="" style="caret-color: rgb(0, 0, 0);">
<br class="" style="caret-color: rgb(0, 0, 0);">
<span class="" style="caret-color: rgb(0, 0, 0);">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.</span><br class="" style="caret-color: rgb(0, 0, 0);">
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<font class="">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.</font>
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<div class=""><span class="" style="">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.</span><span class="" style=""> </span><span class="" style="color: rgb(41, 41, 41); font-family: sohne, "Helvetica Neue", Helvetica, Arial, sans-serif; letter-spacing: -0.016em;"><br class="">
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<span class="" style="caret-color: rgb(0, 0, 0);">Kind Regards</span><br class="" style="caret-color: rgb(0, 0, 0);">
<span class="" style="caret-color: rgb(0, 0, 0);">Ali Hassan Raza</span><br class="" style="caret-color: rgb(0, 0, 0);">
<span class="" style="caret-color: rgb(0, 0, 0);">Roskilde University</span></div>
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