Introduction to Bioimage Analysis using QuPath

Date: September 16th 2024
Time: 10am - 5pm
Location: HMS, Longwood (In-person)
Cost: Free

About

The Image Analysis Collaboratory is running a workshop over one full day. The format will be a combination of tutorials and hands-on exercises.

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.

Participation will be limited to ~20 people.

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

Requirements

None, except a laptop with admin privileges 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.

Scope

  • to digital image analysis, w. focus on bio-images
  • Introduction to QuPath: general concepts (load an image, staining vectors, user-interface)
  • Cell detection, features and cell classification
  • Measurements export
  • Cell classification (machine learning-based)
  • Tissue detection
  • Density maps and spatial measurements
  • Advanced topics (scripts, batch process)

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