slidingwindowinferer for WSI

[shubhaminnani]

Hi,
I am trying to infer WSI in .svs format at 40x magnification, will slidingwindowinferer support WSI with patch size of 256x256?

Thanks,
Shubham

[KumoLiu]

Hi @drbeh, could you please help share some comments on this one?
Thanks in advance!

[bhashemian]

Hi @shubhaminnani, are you referring to SlidingWindowInferer in MONAI? If so, it should work with any patch size as it is has roi_size as an input parameter.

Alternatively, you can use PatchInferer along with SlidingWindlowSplitter and AvgMerger to achieve what you mentioned.
Here you can find some examples for WSI at the end of this tutorial: https://github.com/Project-MONAI/tutorials/blob/main/patch_inferer/modular_patch_inferer.ipynb

[shubhaminnani]

Thank you @drbeh for confirmation of using WSI in .svs format with SlidingWindowInferer. I will check and let you know if any issues.

[bhashemian]

@shubhaminnani, SlidingWindowInferer's input is a tensor already loaded so you need to use WSIReader to load your svs file first (if it fits in memory). Otherwise, use the alternative that I mentioned.

[shubhaminnani]

Sure, Thank you!