Image Analysis with QuPath

Overview

This repository include Material used during "Image Analysis with QuPath" workshops: Presentation, Detailed exercise instructions and related scripts. The image Files are available at or our WIKI page. The Workshop were given at the Weizmann Institute of Science in March 2023

Workshop outline:

1. Create project, load images

2. Inspect meta data

3. Create whole tissue region, Annotations

4. Segment cells – (simple way) StarDist

5. Classify cells – Simple way / ML

6. Region Segmentation

7. Combine Regions & Cells information

8. Export measurements

9. Run for whole project

10. Train Classifiers from representative regions of multiple images

11. BYOD: Bring Your Own Data

    • Presentation & Discussion
    • Work on your own data