check_anonymization

Tool to check anonymization of whole-slide images (WSI). It scans metadata and associated label/macro images for potential PHI.

How to use

• Clone directory anywhere
• Make sure system packages are present
• Open a terminal from the cloned directory
• Install python dependencies

python check_anon.py

• Select folder containing WSI to be checked
• See report

Features

• Choose the input folder via a file-explorer dialog (or pass --input-dir).
• Generates a CSV report with findings.
• Optional OCR on label/macro images using Tesseract.

Requirements

• Python 3.8+
• System packages (Linux, Windows):
  • libopenslide0 (and openslide-tools optional)
  • tesseract-ocr (for OCR; disable by setting RUN_OCR = False in check_anon.py)

Install Python dependencies:

python3 -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

Usage (script)

Using file browser and default location for the report:

python check_anon.py

Specifying paths manually:

python check_anon.py --input-dir /path/to/wsi_folder --report /path/to/report.csv

If --input-dir is omitted, a folder chooser will appear. The report defaults to wsi_anonymization_report.csv in the current directory.

Results

If anonymization is done correctly, everything should be False in the anonymization report (.csv file).