search

ncoudray / DeepPATH

Classification of Lung cancer slide images using deep-learning
492 stars 213 forks source link

Binary masks for svs files #38

Open Tato14 opened 5 years ago

Tato14 commented 5 years ago

Hi,

I am generating binary masks for .svs files. I see in your code that you could use them in .jpg or .dcm files to tile for ROI. Is there any reason it is not possible to do it in svs files?

Also, I do not completely understand to code name I should use. If I have a svs files names "Sample1.svs" the mask name should be "Sample1mask.jpg"?

Thanks

ncoudray commented 5 years ago

Hi -

The only reason why it's not implemented for svs is because we never needed it.

Yes, you should just add mask.jpg and it should work.

I don't have time to properly integrate it to the code right now, but this particular case, if you just replace line 217 with mask, xml_valid, Img_Fact = self.jpg_mask_read(xmldir) It should hopefully work with svs images too (but then will not work for xml, so just change it for this particular case if you're in a hurry).

Best, Nicolas

Tato14 commented 5 years ago

Hi,

Thanks for the quick answer. Unfortunately, I am getting errors in the main function, concretely i'm getting the error: No xml file found for slide Sample1.svs (expected: Sample1.xml). Directory or xml file does not exist from line 806. I tried to add if (ImgExtension == ".jpg") | (ImgExtension == ".dcm") | (ImgExtension == ".svs"): in line 796 and I didn't get the error but I am not getting tiles.

Any idea how to solve it? Thanks!

ncoudray commented 5 years ago

Hmhm.... what's the content of the output log file then?... Also, how are the masked? I think we expect them to be 8 bits with '0' for background and '255' for ROI.