About the extraction of patches using 'cnn_sample'

[joe19981]

When I run 'cnn_sample', the majority of the 500 patches extracted from each Whole Slide Image (WSI) are blank. Is there an issue with this?

[Zhengyushan]

The positions of the patches for extraction are calculated based on the foreground mask of the slide. The magnification (or level) of the mask needs to fit the hyper-parameter 'MASK_LEVEL' in the config file. You may try to tune 'MASK_LEVEL', to the exact LEVEL of your foreground mask.