1:00 PM — 1:20 PM
Presentation of PPBI, LUMC, IRB and Euro-Bioimaging
1:20 PM — 2:00 PM
What is an Image?
2:00 PM — 2:40 PM
Types of images, colormaps and stain vectors
2:40 PM — 2:50 PM
Coffee Break
2:50 PM — 3:30 PM
Concepts of thresholding, ML and DL
3:30 PM — 4:00 PM
QuPath in the world of pathology
9:30 AM — 10:00 AM
How to handle images on QuPath?
  • Image properties
  • Create a project
10:00 AM — 10:45 AM
Tools - Annotations
  • Types of ROIs available and how to use them
  • Hierarchy
  • Properties and Classes
  • Calculating features
  • Exercises
10:45 AM — 11:00 AM
Coffee Break
11:00 AM — 12:00 PM
Tools - Detections
  • Cell detection
  • Properties, Measurements and tips
  • Positive Cell Detection
  • Exercises
12:00 PM — 1:00 PM
Lunch Break
1:00 PM — 1:45 PM
Stain Vectors
  • Setting a stain vector
  • Estimating a stain vector
1:45 PM — 2:45 PM
Pixel Classification
  • Tissue detection
  • Create and measure objects
  • Exercises
2:45 PM — 3:00 PM
Coffee Break
3:00 PM — 3:30 PM
Object Classification
  • Training an object classifier (machine learning)
3:30 PM — 4:00 PM
Density Maps
  • Creating a density map
  • Finding hotspots
  • Creating annotations based on density
9:30 AM — 10:15 AM
Multiplexed analysis
  • Visualization of multiple channels
  • Cell Detection
  • Creating a cell classifier
  • Exercises
10:15 AM — 10:30 AM
Coffee Break
10:30 AM — 11:30 AM
Object Classification
  • Training an object classifier (machine learning)
  • Training images
  • Composite classifiers
  • Improving training
  • Heatmaps
11:30 AM — 12:00 PM
Pixel Classification
  • Training a pixel classifier (machine learning)
  • Creating objects based on classifier
12:00 PM — 1:00 PM
Lunch Break
1:00 PM — 2:00 PM
Introduction to groovy scripting
  • Automated scripts
  • Extensions - Stardist, InstanSeg and Cellpose (deep learning)
2:00 PM — 5:00 PM
Working on your images
  • wrap-up
  • call4help