<div dir="ltr">Hi Ali,<div><br></div><div>Please have a look at this thread from 2014 on this topic: <a href="https://lists.andrew.cmu.edu/pipermail/openslide-users/2014-November/000965.html">https://lists.andrew.cmu.edu/pipermail/openslide-users/2014-November/000965.html</a></div><div><br></div><div>Paraphrasing Benjamin Gilbert's response linked above, the coordinates in the ndpa file are in physical units (nanometers, specifically) relative to the center of the <b>slide</b> as you deduced. You will need to extract the XOffsetFromSlideCentre and YOffsetFromSlideCentre properties from the ndpi image using Openslide. Adding these to each coordinate will yield physical units relative to the center of the main <b>image</b>. (Note the center of the image does not necessarily correlate to the center of the physical slide). Then, you can divide the coordinates by 1000 to yield microns. Using the mpp-x and mpp-y (microns per pixel) Openslide properties for the ndpi image, divide by mpp-[xy] to get pixel coordinates relative to the center of the main image. Finally, subtract by level-0 dimensions / 2 to get into a coordinate space with (0,0) as top-left origin.</div><div><br></div><div><br></div><div>Best,</div><div>Coleman</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 6, 2022 at 1:19 AM Ali Hassan Raza via openslide-users <<a href="mailto:openslide-users@lists.andrew.cmu.edu">openslide-users@lists.andrew.cmu.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;">
<span style="color:rgb(0,0,0)">Hello Openslide members,</span><br style="color:rgb(0,0,0)">
<br style="color:rgb(0,0,0)">
<span style="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 style="color:rgb(0,0,0)">
<br style="color:rgb(0,0,0)">
<font color="#000000">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>
<div><span style="color:rgb(0,0,0)"><br>
</span></div>
<div><span style="color:rgb(0,0,0)">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 style="color:rgb(0,0,0)"> </span><span style="color:rgb(41,41,41);font-family:sohne,"Helvetica Neue",Helvetica,Arial,sans-serif;letter-spacing:-0.016em"><br>
</span><br style="color:rgb(0,0,0)">
<span style="color:rgb(0,0,0)">Kind Regards</span><br style="color:rgb(0,0,0)">
<span style="color:rgb(0,0,0)">Ali Hassan Raza</span><br style="color:rgb(0,0,0)">
<span style="color:rgb(0,0,0)">Roskilde University</span></div>
</div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><table border="0" cellspacing="0" cellpadding="0" style="color:rgb(136,136,136);font-family:Roboto,RobotoDraft,Helvetica,Arial,sans-serif;font-size:13.33px"><tbody><tr><td style="padding:0in"><p style="margin:0in 0in 0pt;line-height:12pt"><span style="color:rgb(35,50,127);letter-spacing:1.2pt;font-family:Arial,sans-serif"><span style="font-size:11.5pt"><b>Coleman Stavish</b></span><span style="font-size:15.33px"><b><br></b></span></span><span style="color:rgb(35,50,127);letter-spacing:1.2pt;font-family:Arial,sans-serif;font-size:9pt">Chief Technology Officer | Proscia</span><b><span style="color:rgb(35,50,127);letter-spacing:1.2pt;font-family:Arial,sans-serif;font-size:11.5pt"><br></span></b><span style="letter-spacing:1.2pt;font-family:Arial,sans-serif;font-size:11.5pt"><span style="letter-spacing:0.5pt;font-size:9pt"><font color="#23327f">+1 610-996-3951<br></font><a href="http://www.proscia.com/" style="color:rgb(17,85,204);font-weight:bold" target="_blank">www.proscia.com</a></span><font color="#23327f"><b><u></u><u></u></b></font></span></p></td></tr><tr style="height:4.5pt"><td style="padding:0in;height:4.5pt"></td></tr><tr style="height:7.5pt"><td style="padding:0in;height:7.5pt"><font size="1">This email and any attachments are confidential and intended solely for the individual to whom they are addressed. If you have received this message in error, please notify the sender immediately and delete this email from your system. Nothing in this email amounts to a contractual or other legal commitment on the part of Proscia.</font></td></tr></tbody></table></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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