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.
Use the package manager pip to install requirements.
pip install requirements.txtSimCLRv2 extractor requires a path to the directory where the model is stored specified in the feature_extractor.py file.
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}