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README.md

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digpath_msi_prediction

Steps for getting patch embeddings

  1. get_filenames.sh

    • Set TOP_LEVEL_DIR to the directory containing the slide-specific subdirectories
    • run with ./get_filenames.sh <label> replacing "label" with 0 or 1 (usually MSS=0, MSI=1)

  2. get_features_CTransPath.py

    • Fill in line 51 with your path to ctranspath.pth
    • Run with python get_features_CTransPath.py <filenames.csv> replacing filenames.csv with the output csv of get_filenames.sh
    • May want to write a shell script to run for all slides' csv files

  3. make_h5.py

    • Set directory to the path to the directory containing the embedding CSVs
    • Set out_directory to the desired output directory for the h5 files
    • Set output_csv to the desired output file for the slide.csv file (an input to HistoBistro)