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MAE implementation

The implementation of MAE is adopted from here, thanks very much!

Extract features from spot patches

  1. Crop the whole histology image to spot patches according to the spatial coordinates, and stack them in npy file. Please note that the size of cropped patches should be 224*224.

  2. run MAE to extract features

# Set the path to save images
OUTPUT_DIR='output/'
# path to image for visualization
PATCHES_PATH='/path/to/cropped/patches.npy'
# path to pretrain model
MODEL_PATH='/path/to/pretrain/checkpoint.pth'


python run_mae_extract_feature.py ${PATCHES_PATH} ${OUTPUT_DIR} ${MODEL_PATH}

Pretrained Weights

The pretrained weights can be found using the link from the original repository here