Basic image processing using Fiji
Basic image processing using Fiji
12 June 2026, 9h30-17h00
General context
As microscopy has become central to life science research, the ability to process and analyze image data is essential for PhD students, postdocs, and technical staff working with biological images. This introductory training offers a hands-on approach to image processing with Fiji, an open-source platform based on ImageJ.
You will learn to perform basic image processing tasks, apply filters, and use plugins for biological image quantification. This includes using built-in machine learning and neural network methods for image segmentation tasks. The course also covers automating repetitive tasks with macros, enabling more efficient and reproducible workflows. By the end of the session, you will have the practical skills to analyze microscopy images and develop simple analysis pipelines for your research.
- Identify core Fiji interface components and describe their functions in image analysis.
- Apply standard image processing operations (e.g., filtering, thresholding, segmentation).
- Use key Fiji plugins for common life science image analysis tasks.
- Evaluate image analysis quality and accuracy by comparing processed and raw data.
- Create simple image analysis workflows and build a Fiji macro for batch processing.
- Modify existing macro scripts to specific experimental needs.
This course uses a strong hands-on approach with guided exercises in Fiji.
Experienced ImageJ users may find limited novelty in the content.
No prior knowledge is required to join this course. Participants are requested to bring their own laptops pre-installed with Fiji.
Fiji
This course is part of the learning path Bioimaging.
AI methods used
The course explores machine learning and neural network methods for image segmentation, covering Random Forest–based pixel classification with Trainable Weka Segmentation and a neural network for nucleus segmentation (StarDist). The course includes demonstrations of cell segmentation (Cellpose) and general-purpose object segmentation (Segment Anything Model - SAM).
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
Morning session: Image basics and basic operations
Image properties, pixel operations, filters, segmentation, ROI's, registration, pixel classification, and more.
Introduction to ImageJ1 macro language
Practical info
12 June 2026
Antwerp - Campus Drie Eiken UAntwerpen
Universiteitsplein 1
2610 Antwerpen
Belgium
12 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.
12 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.
12 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.