Teach your computer to see objects on bioimages with Ilastik
Teach your computer to see objects on bioimages with Ilastik
3 June 2026, 9h30 - 17h00
General context
Many experimental biologists and imaging facility users need to perform sophisticated segmentation of microscopy images, such as distinguishing between different cell structures or quantifying objects in dense, noisy backgrounds. Classical methods (thresholding, watershed, and manual annotation) often struggle with the variability and complexity of bioimage datasets. Ilastik provides an accessible machine-learning-based solution, allowing pixel- and object-level classification and integrating seamlessly with Fiji for downstream image processing, quantitative analysis, and batch processing across multiple images
- Explain the principles of supervised machine learning for pixel and object classification in microscopy images.
- Create and annotate pixel and object classifiers in Ilastik for simple segmentation and classification tasks.
- Export Ilastik probability maps and segmentations for further analysis in Fiji.
- Set up and use the Ilastik Fiji plugin for batch processing and automating pipelines for multi-image datasets
- Apply pre-trained models from the BioImage Model Zoo and adapt them to their data
This course uses a strong hands-on approach with guided exercises in Ilastik and Fiji
No formal programming or machine learning expertise is required, but you should:
- Be familiar with visualizing and processing microscopy images using Fiji. If you have no experience, you can follow our training on Basic image processing using Fiji.
- Have some basic understanding of the biological structure of interest (e.g., nuclei, cells, tissues) to inform annotation and classifier setup.
- Ilastik (latest release, Windows/ Mac/ Linux)
- FIJI with the Ilastik FIJI plugin (for direct integration/ export/ import, especially to handle large datasets and automate pipelines).
This course is part of the learning path Bioimaging.
AI methods used
This course applies supervised machine learning methods using Random Forest for image segmentation and classification, using pixel- and object-level models trained on user-provided annotations. Participants will work with pre-trained and custom models to generate probability maps and segmentations, without requiring in-depth knowledge of model development
Trainers
Practical info
03 June 2026
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
03 June 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.
03 June 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).
03 June 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.