GUIDE

AI model for calculating gemistocytic astrocytes percentage of whole slide images.

Create environment

git clone https://github.com/WangLabHKUST/GUIDE
cd GUIDE
conda env create -f environment.yml
conda activate guide

File organization

Input: PATH_TO_WSI_FILES (prepare your inputs here)
    --slide1.npdi
    --slide2.ndpi
Output: OUTPUT_PATH       
	--mask
	  --filter_png
	  	--slide1.ndpi-...-filtered.png
		--slide2.ndpi-...-filtered.png  
	  --... (other intermediate files)
    --h5
      --slide1.h5
      --slide2.h5
    --results
      --slide1.h5_detailed_results.csv
      --slide2.h5_detailed_results.csv
MODEL_PATH: download pretrained model weight here

Pretrained model weight can be downloaded here

https://drive.google.com/file/d/1RFpyRKg66l9b4050NTLfMRctsWVVuevp/view?usp=sharing

Quick run

sh demo.sh