andreped
commented
2 years ago First, regarding the strange zero-padded regions. I think that is actually part of the original image. Could you open it in QuPath and verify that you get the same?
The reason why it might be especially slow, is because the zero-padded regions are assumed to be tissue, as glass is filtered depending on how far away it is from the color white. I could add an option to include uint 0 in the glass class to be filtered.
Also, you opened both these in FP, right? The same WSI in the MRXS and TIFF format, right? Could you send me the prompts for both? Include all. I don't care about inference, just what is displayed when opening the WSI.
I assume that the wrong magnification is used somehow for the MRXS format. If so, it could be quick to fix.
Also, for the TIFF image, the segmentation looks OK, was this without extracting the H-image?
pr4deepr
Thought its better to create a new issue instead of using the other one for mrxs file format https://github.com/AICAN-Research/FAST-Pathology/issues/6#issuecomment-1007166721
I can open a mrxs file in FP now, but the file opens like this:
When I run predictions using the Epithelium models in NoCodeSeg, it takes a while and the end result looks like this on an inset:
However, when I export the mrxs file to a tiled-tiff using the CaseViewer software, followed by conversion in vips to a pyramidal tiff (jpeg, quality = 85), and then run predictions, I get this:
The image magnification is 10 for both.
I could share the dataset with you but will have to be via email. We wouldn't need any agreements. Its just that I can't share it directly as its a cross-institutional project. The owner will have to share it with you directly.
Cheers Pradeep