Basic image processing using Fiji
Basic image processing using Fiji
30 January 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.
This course is designed for researchers working with microscopy images who have little to no experience in image processing. Experienced Fiji 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
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
Program
Morning session: Image basics and basic operations
Introduction to ImageJ1 macro language
Practical info
30 January 2026
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
30 January 2026
Leuven - Campus Gasthuisberg
Leuven train station is approximately 4 km from the campus Gasthuisberg. Buses depart very regularly to the Gasthuisberg Campus from Leuven train station.
For tickets and up to date schedules visit website De Lijn or use the De Lijn App.
Exit at the very last bus stop ‘Gasthuisberg Campus) make sure not to exit at ‘Gasthuisberg Kliniek =
hospital)
Once you get off the bus, go to your right and go up the street until you see stairs to your left. Climb the stairs all the way up between two buildings. Look for the signs containing blue circles and white numbers and follow them all the way from 2 up to number 12. You will cross several buildings and the walk will take max. 10 minutes. When you reach number 12, you have reached O&N 5, where you can find the reception.
30 January 2026
Leuven - Campus Gasthuisberg
The Gasthuisberg campus is west of the Leuven ring. Our buildings are situated behind the hospital (see black arrow near ‘RING NOORD’ on the map). If you come from the city center, you will arrive on campus from the east side (taking Mgr. Van Waeyenberglaan and roundabout Het Teken). If you come from Heverlee or Campus Arenberg, you will arrive from the west side (taking the Celestijnenlaan and Taborweg). When you arrive uphill at the intersection with the Rega Institute and the Red Cross building, you need to take the road down to the bicycle parking at Rega Institute (see map) where you can park. Next, follow the ‘Onderwijs & Navorsing blue route’ description below (start point is #9).
30 January 2026
Leuven - Campus Gasthuisberg
You arrive via the E314 highway – EXIT 16
After 200 m, keep left to drive underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
You arrive via the Leuven ring road
At the roundabout, take the exit towards ‘Spoed / Ziekenhuis’.
Follow the ring around Campus Gasthuisberg and pass the entrance of SPOED.
Continue right until you arrive at a second roundabout.
Follow the directions for E314.
Near the Fire Brigade Station, make a U-turn and follow the directions for ‘Ziekenhuis’.
Keep left and drive downhill, underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
Next, leave the parking at level +1 using the big stairs near the vending machines.
Follow the red carpet and arrows to 'Onco Dagcentrum' to get to the O&N buildings. Take the stairs on your left after exiting Parking West. You are now in front of the O&N4 building; on the left you will find O&N5.