QuPath: quantitative pathology & bioimage analysis software

QuPath: quantitative pathology & bioimage analysis software

17 October 2025

Ghent - VIB/UGent FSVM II | room L4

hands-on
imaging
software
live training

QuPath: quantitative pathology & bioimage analysis software

Target Audience:
VIB PhD student
VIB postdoc
VIB staff scientist
VIB group leader or expert
VIB technical support
Flemish academic or researcher
Non-Flemish academic or researcher
Industry professional
Location:

Ghent - VIB/UGent FSVM II | room L4

Duration:

17 October 2025, 9h30- 17h00

General context

This introductory QuPath course is designed for early-stage researchers—particularly 1st-year PhD students, postdocs, and research support staff—who are new to digital pathology and image analysis. As high-throughput imaging becomes increasingly central to biomedical research, the ability to efficiently analyze whole slide images (fluorescent and histochemical) is essential. This training provides a hands-on introduction to QuPath, a powerful open-source platform for bioimage analysis and specifically large 2D images such as slide scanner images. Participants will learn how to navigate the software, annotate images, perform cell segmentation, classify pixels and objects, and extract quantitative features. The course also introduces basic scripting for batch processing, enabling scalable workflows. By the end of the session, attendees will be equipped to independently analyze their own slide scanner images (histochemical and fluorescent) and integrate image analysis into their research pipelines.

Learning outcomes
  • 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 automate repetitive tasks and batch process multiple images.
Event intended for

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.

Required skills

No previous experience is required. Participants are requested to bring their own laptop, with QuPath pre-installed. 

Software demonstrated

QuPath

Trainers

Benjamin Pavie
VIB Bioimaging Core, BE
Amanda Gonçalves
VIB Bioimaging Core Ghent, BE

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.

Nicolas Peredo
VIB BioImaging Core Leuven, BE

Nicolas Peredo is a microscopy and image analysis trainer at the VIB Bioimaging Core in Leuven.

Program

QuPath basic
-
QuPath scripting + User dataset analysis
-

Practical info

Location & Venue

17 October 2025

Ghent - VIB/UGent FSVM II

Technologiepark 75
9052 Zwijnaarde
Belgium

Public transport

17 October 2025

Ghent - VIB/UGent FSVM II
Public transport

From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.

Bike

17 October 2025

Ghent - VIB/UGent FSVM II
Bike

Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
 

Shared bicycles:

Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic

There are also some public bicycle pumps at the park.

Route description

17 October 2025

Ghent - VIB/UGent FSVM II
Parking

Route description

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.

Venue contact

17 October 2025

Ghent - VIB/UGent FSVM II