Quantitative bioimage analysis in QuPath: Essentials
Quantitative bioimage analysis in QuPath: Essentials
2 October 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
Benjamin Pavie
Amanda Gonçalves
Amanda is a Microscopy Expert at the VIB Bioimaging Core-Gent, where since 2011, she has gained expertise in large sample imaging and quantification, from slide scanner to light sheet. She also has over 15 years of experience teaching science, both practical and theoretical, on the graduate and post graduate levels.
Program
QuPath basic
QuPath scripting + User dataset analysis
Practical info
02 October 2026
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
02 October 2026
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
02 October 2026
Ghent - VIB/UGent FSVM II
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Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
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- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
02 October 2026
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.