Bioimage analysis in Python
Bioimage analysis in Python
21 April 2026, 09h00-17h00
22 April 2026, 09h00-17h00
General context
Microscopy generates complex, multi-dimensional image data that requires efficient analysis to extract meaningful biological insights. This hands-on training teaches you practical skills for handling and processing microscopy images using Python.
You will learn to visualize, manipulate, and analyze image data using tools such as Napari, allowing you to explore 2D and 3D datasets interactively. With built-in tools like Cellpose and Noise2Void, you will learn to leverage deep learning methods for bioimage analysis tasks like image segmentation and quantitative analysis.
Navigate the Napari interface to visualize and interact with multi-dimensional microscopy images
Import and export image data using Napari and Python libraries (e.g., bioio, NumPy) while preserving metadata
Apply basic image processing techniques (e.g., filtering, intensity adjustments) within Napari
Compute and plot quantitative descriptors (e.g., intensity histograms, object counts) for segmented images to support data analysis.
Segment microscopy images using both classical approaches and automated tools to identify biological objects.
Generate simple animations to communicate image analysis results.
This course uses a strong hands-on approach with guided exercises in Napari. We install and use Napari plugins to extend functionality for segmentation and analysis tasks.
Basic knowledge of Python programming and ability to work with Python environments (understanding of syntax, data structures, data handling, and basic plotting. This can be acquired by completing our Python introduction e-learning. Send a mail to trainingandconferences@vib.be and we'll give you access to the material.
- Napari
- The libraries covered will be CellPose, scikit-image, bioio (list non-exhaustive)
This course is part of the learning path Bioimaging.
AI methods used
The course covers deep learning methods for bioimage analysis, including Cellpose for object segmentation and Noise2Void, a self-supervised neural network for image denoising. It also introduces classical image processing methods for comparison with machine learning–based approaches.
Trainers
Practical info
21 April 2026 - 22 April 2026
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
21 April 2026 - 22 April 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.
21 April 2026 - 22 April 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).
21 April 2026 - 22 April 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.