Description
Hey all!
I have a question about the usage of CLAM.
I have a dataset of about 500 histological images of brain regions with iron staining. These images are already downscaled by a factor of 20x and then segmented. This means that I am not using pyramidal TIFFS but already segmented 3000x3000 jpgs. I have noticed that this framework is not entirely designed for this use case, but I think it will work fine!
I'm currently struggling with tweaking the parameters for this specific dataset. Using patches of 256x256 and a line thickness of 250 just creates ridiculous images like this one below
That is why I want to use patches of about 16x16. However, I don't seem to be able to make that work with the create_patches_fp.py. Currently, it seems to make a grid of 16 patches of where the original tissue seems to be, like this.
The parameters I have used for this result is the bwh_resection preset, with a patch size of 16.
In general, I feel a bit lost when it comes to changing these parameters in the script.
- The seg_ and vis_level are not so interesting for me, as I only have 1 image.
- The line thickness should not be much more than 5 pixels, I think
- max_n_holes is not that interesting for me, as I don't have that many holes in my segmentation. It is mostly one piece of tissue.
For the rest of the parameters, I feel a bit clueless as to what it exactly does. Although it feels like the parameters don't really change that much, and I just end up with the small pixel grid all the time.