Basic image processing using Fiji
18 June 2025, 9h30-17h00
General context
As microscopy becomes increasingly central to life science research, the ability to process and analyze image data is essential for early-stage PhD students, postdocs, and technical staff working with biological images. This training introduces participants to Fiji, a widely used open-source platform built on ImageJ, designed for scientific image analysis. Through hands-on exercises, participants will learn how to perform basic image processing tasks, apply filters, and use plugins for biological image quantification. The course also covers the use of macros to automate repetitive tasks, enabling more efficient and reproducible workflows. By the end of the session, attendees will be equipped with practical skills to independently analyze microscopy images and build simple analysis pipelines tailored to their research needs.
- Identify the basic components of the Fiji interface and describe their functions in image analysis.
- Apply standard image processing operations (e.g., filtering, thresholding, segmentation) to biological images using Fiji.
- Demonstrate the use of key Fiji plugins for common image analysis tasks relevant to life sciences.
- Construct a simple image analysis workflow using the Fiji macro language to automate repetitive tasks.
- Evaluate the quality and accuracy of image analysis results by comparing processed outputs with raw data.
- Modify existing macro scripts to adapt analysis pipelines to specific experimental needs.
This course is designed for researchers working with microscopy images who have little to no experience in image processing. 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 laptop, Fiji pre-installed.
Fiji
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
18 June 2025
Antwerp - Campus Drie Eiken UAntwerpen
Universiteitsplein 1
2610 Antwerpen
Belgium
18 June 2025
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.
18 June 2025
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.
18 June 2025
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.
18 June 2025
Antwerp - Campus Drie Eiken UAntwerpen
Neuron Room (D.VA.224)
VIB Center for Molecular Neurology - Building V of the University of Antwerp (UA) - CDE, Parking 4, Universiteitplein 1, B-2610 Antwerpen