COURSE | INTRODUCTION TO QUPATH SOFTWARE
OVERVIEW | This course intends to give a brief introduction (Theoretical & Practical) to the use of QuPath (free open-source software for "Quantitative Pathology") for analysis of tile & stitched large image datasets, such as those obtained at slide scanners from the Histopathology and Bioimaging Units.
DATES & VENUE | 21st - 23rd May 2025 @ RISE-Health, University of Beira Interior, Covilhã (Portugal)
HYBRID | online plenary lectures (21st May) + practical sessions in person on each node + online tutorials (22nd-23rd May)
COST | Free
REGISTRATION DEADLINE | 11th May 2025, limited to 10 participants
REQUIREMENTS | Bring your own laptop + transformer + mouse / Course Material (Images + Models + Extensions) - on folder provided / Install QuPath [https://github.com/qupath/qupath/releases]
Participants will be notified of course acceptance on the 12th May 2025 by email.
If you have any questions, please contact us: rise-ubi.microscopia@fcsaude.ubi.pt.
PRELIMINARY PROGRAMME
Day 1 | 21st May
Session I - Introduction to image analysis
14h00 - 14h15 Presentation of PPBI
14h15 - 14h55 What is an Image?
14h55 - 15h35 Types of images, colormaps and stain vectors
15h35 - 15h50 Coffee Break
15h50 - 16h30 Concepts of thresholding, ML and DL
16h30 - 17h00 QuPath in the world of pathology
Day 2 | 22nd May
Session II - Introduction to QuPath
09h30 - 10h15 How to handle images on QuPath?
10h15 - 11h15 Tools - Annotations
11h15 - 11h30 Coffee Break
11h30 - 12h30 Tools - Detections
12h30 - 14h00 Lunch Break
Session III - Brightfield Images
14h00 - 14:45 Stain Vectors
14h45 - 15h45 Pixel Classification
15:45 - 16:00 Coffee Break
16:00 - 16:30 Object Classification
16h30 - 17:30 Density Maps
Day 3 | 23rd May
Session IV - Fluorescence Images
09h30 - 10:30 Multiplexed analysis
10h30 - 11h30 Object Classification
11h30 - 11h45 Coffee Break
11h45 - 12h15 Pixel Classification
Session V - Automated workflows
12h15 - 13:00 Introduction to groovy scripting
13h00 - 14h00 Lunch Break
Session VI - Call4Help (Optional)
14:00 - 16:00 Working on your images