WSI-anonymity

Tools for analysis of privacy risks related to sharing Whole Slide Images in digital pathology research. The code has been used for the research paper available at https://www.medrxiv.org/content/10.1101/2022.04.06.22273523v3.

Installation

Use the package manager pip to install requirements.

pip install requirements.txt

SimCLRv2 extractor requires a path to the directory where the model is stored specified in the feature_extractor.py file.

Usage

Data needs to be in PNG format. The map file contains a pickled list of patients. Each patient is represented by a list of its PNG filenames.

python anonymity.vpi_block_subset
    --slide_dir {data_directory}
    --map_path {pickled_map_path}
    --extractor {extractor}
    --metric {metric}