dtruhn / PathStruct

Code and Data for "Extracting Structured Information from Unstructured Histopathology Reports with GPT-4"

Extracting Structured Information from Unstructured Histopathology Reports with GPT-4

Install

Depending on your setup you have to install the following:
sudo apt-get install tesseract-ocr

Create virtual environment and install packages:
python -m venv venv
source venv/bin/activate
pip install -e .

Get Started

1 ChatGPT API Key

• create a file secret_api_key.txt in the root folder (next to this file) and copy your secret API key inside

2 Prepare data

• place all your pdf-files under data/reports

3 Extract text from data

• Run scripts/pdf2text.py

4 Create structured report from text

• Run scripts/text2report.py