Introduction to Bioimage Analysis using QuPath

Sep 16, 2024

Workshop poster

Past workshop material

About:

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 is running a workshop over one full day. 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).

Time:

Monday September 16th, and from 10 AM to 5 PM

Place:

Harvard Medical School in Longwood, Boston, MA.

Format:

In-person.

Skill level:

Beginner

Requirements:

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, please apply for the next workshop.

Scope:

  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
  5. Cell classification (machine learning-based)
  6. Tissue detection
  7. Density maps and spatial measurements
  8. Advanced topics (scripts, batch process)

Cost:

Free of charge.

Applying:

Please apply here.
If you have any questions, please feel free to reach out to Antoine Ruzette.

Deadline for application:

11:59 PM on Sunday, 1st September 2024

Selection:

Mostly based on your short motivation. In case of oversubscription, the available spaces will be distributed evenly between labs and departments.

NB

Our workshops are often oversubscribed by a factor of two or three, so please be considerate to your fellow applicants and let us know well in advance if you are accepted and cannot make it.

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

QuPath