README.md

Dependencies

pip install -r requirements.txt

Training

First prepare the training images, run

cd data
python img_prep.py --source-folder path_to_source --target-folder path_to_target
cd -

To train the model, simply run

# request excution permission for the first time
chmod +x train.sh

./train.sh

Be aware that you can specific a image to plot during training by setting the --test-img argument in train.sh.

Inference

We provide the infer method in the train.py for online inference. First provide images of RGB H&E slide, necrosis.png and perfusion.png; Then run the following command to predict the hypoxia output. The output will be saved as predict.png.

python train.py --infer \
        --patch-size 128 \
        --model path_to_checkpoint_file \
        --test-img path_to_source_images