QuPath: quantitative pathology & bioimage analysis software
QuPath: quantitative pathology & bioimage analysis software
23 January 2026, 9h30-17h00
General context
As high-throughput imaging becomes increasingly central to biomedical research, the ability to efficiently analyze whole slide images is essential. This training provides a hands-on introduction to QuPath, a powerful open-source platform for bioimage analysis.
You will learn how to navigate the software and leverage built-in machine learning algorithms (including Random Forest and neural networks) to perform cell segmentation, classify pixels and objects, and extract quantitative features. We will also introduce basic scripting for batch processing, enabling scalable workflows.
- Identify the core functionalities of QuPath, including image management, annotation tools, and project organization.
- Apply cell segmentation techniques to detect and quantify cellular structures in whole slide images
- Classify tissue regions using pixel classification tools based on staining patterns and morphological features.
- Extract quantitative features from annotated regions to support downstream statistical analysis.
- Differentiate between object classification strategies and implement them to label biological structures.
- Execute basic QuPath scripts to batch process multiple images.
This course uses a strong hands-on approach with guided exercises in QuPath.
This course is designed for researchers who use or plan to use a slide scanner and would like to process and analyze their data.
No previous experience is required. Participants are requested to bring their own laptop, QuPath pre-installed.
QuPath
This course is part of the learning path Bioimaging.
AI methods used
The course covers supervised machine learning methods using feature-based algorithms such as Random Forest and other OpenCV-integrated models. It also introduces neural network methods of segmentation with StarDist. Cellpose and the Segment Anything Model (SAM) are demonstrated during the course.
Trainers
Program
QuPath basic
QuPath scripting + User dataset analysis
Practical info
23 January 2026
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
23 January 2026
Leuven - Campus Gasthuisberg
Leuven train station is approximately 4 km from the campus Gasthuisberg. Buses depart very regularly to the Gasthuisberg Campus from Leuven train station.
For tickets and up to date schedules visit website De Lijn or use the De Lijn App.
Exit at the very last bus stop ‘Gasthuisberg Campus) make sure not to exit at ‘Gasthuisberg Kliniek =
hospital)
Once you get off the bus, go to your right and go up the street until you see stairs to your left. Climb the stairs all the way up between two buildings. Look for the signs containing blue circles and white numbers and follow them all the way from 2 up to number 12. You will cross several buildings and the walk will take max. 10 minutes. When you reach number 12, you have reached O&N 5, where you can find the reception.
23 January 2026
Leuven - Campus Gasthuisberg
The Gasthuisberg campus is west of the Leuven ring. Our buildings are situated behind the hospital (see black arrow near ‘RING NOORD’ on the map). If you come from the city center, you will arrive on campus from the east side (taking Mgr. Van Waeyenberglaan and roundabout Het Teken). If you come from Heverlee or Campus Arenberg, you will arrive from the west side (taking the Celestijnenlaan and Taborweg). When you arrive uphill at the intersection with the Rega Institute and the Red Cross building, you need to take the road down to the bicycle parking at Rega Institute (see map) where you can park. Next, follow the ‘Onderwijs & Navorsing blue route’ description below (start point is #9).
23 January 2026
Leuven - Campus Gasthuisberg
You arrive via the E314 highway – EXIT 16
After 200 m, keep left to drive underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
You arrive via the Leuven ring road
At the roundabout, take the exit towards ‘Spoed / Ziekenhuis’.
Follow the ring around Campus Gasthuisberg and pass the entrance of SPOED.
Continue right until you arrive at a second roundabout.
Follow the directions for E314.
Near the Fire Brigade Station, make a U-turn and follow the directions for ‘Ziekenhuis’.
Keep left and drive downhill, underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
Next, leave the parking at level +1 using the big stairs near the vending machines.
Follow the red carpet and arrows to 'Onco Dagcentrum' to get to the O&N buildings. Take the stairs on your left after exiting Parking West. You are now in front of the O&N4 building; on the left you will find O&N5.