README.md

Artificial Intelligence Unravels Interpretable Malignancy Grades of Prostate Cancer on Histology Images

CONTENT

• You need a source-code editor (e.g., Visual Studio Code from https://code.visualstudio.com)

• Python ≥3.8 (Either built-in or from https://www.python.org)

• Jupyter notebook (How to install: https://jupyter.org/install)

• Packages installation:
  https://github.com/oeminaga/AI_PCA_GRADE/blob/main/install_packages.sh
  

• Extraction of TMA core images

  • Download QuPath
    https://qupath.github.io
  • The instruction given by Andrew Janowczyk
    http://www.andrewjanowczyk.com/de-array-a-tissue-microarray-tma-using-qupath-and-python/
    

• Neural Architecture Search:
  https://github.com/oeminaga/AI_PCA_GRADE/blob/main/NAS_PlexusNet.ipynb
  

• Model development and inference on TMA images
  https://github.com/oeminaga/AI_PCA_GRADE/blob/main/main_notebook_for_model_development.ipynb
  

• Inference on whole-slide images with support for parallel computing-processing multiple whole slide images at the same time- (the ImageScope's xml annotation file including the demarcation of cancer lesions is required)

  • Aperio ImageScope (Image Viewer and Annotion Tool):
    https://www.leicabiosystems.com/us/digital-pathology/manage/aperio-imagescope/
    
  • SCN files:
    https://github.com/oeminaga/AI_PCA_GRADE/tree/main/PROCESS_SCN_WSI
  • SVS files:
    https://github.com/oeminaga/AI_PCA_GRADE/tree/main/PROCESS_SVS_WSI
    
  • TIFF and other formats: ⚙️🚧

• Statistical analyses -abstract version for clarity-
  

  • Survival analyses and comparsion of cox models:
    https://github.com/oeminaga/AI_PCA_GRADE/blob/main/Analysis/evaluation.R
    
    • Please use R Studio to open this file. To install, please follow the instruction given in the link [https://posit.co/download/rstudio-desktop/]
  • Distribution of 64 representation features for our novel model:
    https://github.com/oeminaga/AI_PCA_GRADE/blob/main/Analysis/FeatureDistributionAnalysis.ipynb
    

Should you have issues, please open a thread in the issue section.

Please cite the following paper when you use these scripts [https://www.nature.com/articles/s44303-023-00005-z?utm_source=rct_congratemailt&utm_medium=email&utm_campaign=oa_20240306&utm_content=10.1038/s44303-023-00005-z]