Introduction to Bioimage Analysis using QuPath


QuPath is a user-friendly, cross-platform, open-source software designed for digital pathology and whole slide image analysis. Since its initial release in 2017, it has become an essential tool for researchers who analyze brightfield (H&E, H-DAB) and fluorescence images.

The Image Analysis Collaboratory and Nikon Imaging Center are running a workshop over two afternoons. Participation will be limited to 20 people. The format will be a combination of tutorials and hands-on exercises (you will need a laptop with a decent size screen and admin privileges).


Monday 20th and Tuesday 21st May 2024 from 1 PM to 4 PM.


Harvard Medical School.



Skill level:



None, except a laptop and interest in learning some bioimage analysis.
If you are already somewhat advanced (you code your own workflows), this level is perhaps not for you, though you might want to learn about QuPath specifically.
Participation both days is required—if you can only make it one of the days, don’t apply.


First half-day:

  1. Introduction to digital image analysis, w. focus on bio-images
  2. Introduction to QuPath: general concepts (load an image, staining vectors, user-interface)
  3. Cell detection, features and cell classification
  4. Measurements export

Second half-day:

  1. Cell classification (machine learning-based)
  2. Tissue detection
  3. Density maps and spatial measurements
  4. Advanced topics (scripts, batch process)


Free of charge.


Application will open in the coming weeks. Join our mailing list to get notified when applications open. If you have any questions, please feel free to reach out to Antoine Ruzette.

Looking forward to see you there
Antoine Ruzette, Federico Gasparoli, Ranit Karmakar, Maria Theiss, and Simon F. Nørrelykke.