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I am wanting to use MONAI's SlidingPatchWSIDataset to extract patches from my whole slide images during inference. However, I also require the WSI to be masked so as to remove the unwanted background patches from analysis. Is there any way to incorporate the two?

I am using Otsu's thresholding method to create my tissue mask at an MPP of 16 (currently save in both numpy file and geoPandas df as a polygon), and am wanting my patches to be extracted at mpp of 1.008. How do I use this mask in my dataset?

These two classes look very useful but I cannot find any examples of their usage online.

本文标签： pythonMONAI How to incorporate SlidingPatchWSIDataset with MaskedPatchWSIDatasetStack Overflow

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