Why are only 0 coordinates extracted?

[lsnls]

Hello, authors!

Thank you for your valuable work! When I run extract_patches.py, one of the slides extract 0 coordinates. The detailed information is provided below. Could you please explain why this is happening?

Creating patches for:  TCGA-60-2720-11A-01-BS1.ee2affdb-1df7-49a6-b0ba-bb6767bc613f ...
Total number of contours to process:  1
Bounding Box: 29568 22474 6801 5699
Contour Area: 4966136.0
Extracted 0 coordinates
segmentation took 0.23748326301574707 seconds
patching took 0.03165268898010254 seconds
stitching took -1 seconds 

Thank you a lot. Looking forward to your reply.
Suoni

[his0car]

Total number of contours to process: 1
It seems like the segmentation parameters aren't suited to the image

[lsnls]

Hi, @his0car, Thank you for your help.

Total number of contours to process is greater than 0, so why are no coordinates extracted? Thank you again.

[his0car]

I don't know. Maybe it is smaller than the patch size. Add --seg to your create_patches_fp.py command and have a look at the segmentation mask

[lsnls]

Hi, @his0car , I am sorry for not showing the complete command that I ran. In fact, I ran python create_patches_fp.py --source source_dir --save_dir save_dir --patch_size 1024 --step_size 1024 --seg --patch --stitch --patch_level 1 --preset tcga.csv. I processed many WSIs at the same time, and only one WSI encountered the problem. Thank you again for your help.

[his0car]

As you used --seg, the segmentation mask was saved. Have a look at it and compare it to the others, you will probably have to adjust your segmentation parameters for this particular WSI. Also, if it is just one WSI, then you can also discard it, but I suspect when one fails there may be others that also have bad segmentation.

[lsnls]

Thank you for your advise. I will try.