Quantitative bioimage analysis in QuPath: essentials
Quantitative bioimage analysis in QuPath: essentials
11 June 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 intended for researchers who are using or planning 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
Benjamin Pavie
Bob Asselbergh
Bob is staff scientist at the VIB Center for Molecular Neurology’s Bio-Imaging Expertise Unit, with an interest in quantitative fluorescence assays, automated high throughput microscopy and superresolution expansion microscopy.
Program
QuPath basic
QuPath scripting + User dataset analysis
Practical info
11 June 2026
Antwerp - Campus Drie Eiken UAntwerpen
Universiteitsplein 1
2610 Antwerpen
Belgium
11 June 2026
Antwerp - Campus Drie Eiken UAntwerpen
Antwerp has a dense public transportation network. Buses and trams are available to take you to many different parts of the city. There are direct bus links to various other towns and cities as well. Plan your route using the De Lijn timetables.
- Campus Middelheim - Campus Groenenborger: around 7 min. on foot
- Campus Middelheim - Campus Drie Eiken: around 35 min.
- Campus Groenenborger - Campus Drie Eiken: around 45 min.
- Stadscampus - Campus Middelheim: around 45 min.
- Stadscampus - Campus Groenenborger: around 55 min.
- Stadscampus - Campus Drie Eiken: around 60 min.
Did you know Antwerp also has a water bus? You can use it to travel between the Antwerp city centre and nearby towns.
11 June 2026
Antwerp - Campus Drie Eiken UAntwerpen
Antwerp is a bike-friendly city. Get to know the smart and cheap way to travel around in Antwerp fot students.
For short trips in and around the city, a rental bike is ideal. Apart from the student bicycle and the Velo city bikes, there are several other bike rental options.
Do you need to cross the Scheldt? Check the availability of the bike lifts and escalators of the tunnels, or take Antwerp’s ferry service with your bike.
Cycling between campuses:
- Stadscampus - Campus Middelheim: 20 min.
- Stadscampus - Campus Groenenborger: 25 min.
- Stadscampus - Campus Drie Eiken: 30 min.
- Campus Middelheim - Campus Groenenborger: 4 min.
- Campus Middelheim - Campus Drie Eiken: 10 min.
- Campus Groenenborger - Campus Drie Eiken: 8 min.
The newest way to travel around Antwerp is by shared electric scooter.
11 June 2026
Antwerp - Campus Drie Eiken UAntwerpen
It’s recommended to travel to and in Antwerp by public transport. If you are travelling by car, take the following into account:
- There are P+R zones where you can park on various main roads into Antwerp. They are ideal places to switch to bus, tram or bike a few kilometres from the campus.
- The Antwerp city centre and part of Linkeroever (Antwerp’s left bank) are a low-emission zone: highly polluting vehicles are not allowed into the city.
- Keep in mind that the zone around the Stadscampus is a residential area with a speed limit of 20 km/h. Pedestrians freely make use of the entire road.
- Take possible road works and events into account.
- Within Antwerp, you can make use of the taxi service.
Campus Drie Eiken en Campus Groenenborger have free university parking spots.
Carpooling is not only fun and ecological, but also good for your wallet and you get to meet new people. Are you looking for a car ride or a fellow passenger, occasionally or daily? Take a look at our carpool platform.