Need help urgent
zhaoy at motic.com
zhaoy at motic.com
Wed Jul 6 01:31:06 EDT 2022
Is there any example data we can try to help ?
On Jul 6, 2022, at 1:18 PM, Ali Hassan Raza via openslide-users <openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu>> wrote:
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.
Ali Hassan Raza
openslide-users mailing list
openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu>
只有有权接收电子邮件中可能包含的机密信息的用户才能接收此电子邮件。从 @motic.com 传递的电子邮件可能包含机密信息和法律特许的信息。如果您不是此邮件的预期收件人，请勿阅读、复制、转发或存储此邮件。如果已误收此邮件，请将其转发到发件人，并从您的计算机系统彻底删除此邮件。
This message from @motic.com's email system is for the designated recipient only and may contain privileged, propritary, or otherwise private information. If you received it error, please notify the sender immediately and delete the original. Any other use of this email by you is prohibited.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the openslide-users