Bioimaging data analysis using High Performance Computing (HPC)
Bioimaging data analysis using High Performance Computing (HPC)
18 September 2025, 9h30-17h00
19 September 2025, 9h30- 12h00
General context
Asa datasets grow in size and complexity, traditional desktop tools often fall short. This introductory training shows you how to leverage the Flemish Supercomputer Center (VSC) infrastructure for efficient and reproducible image analysis. It is intended for scientists who work with microscopy or bioimage data and want to scale up their analysis using high-performance computing (HPC)
You will learn to access HPC resources via the Open OnDemand portal, run GUI-based tools (like napari or Fiji), and adapt existing pipelines (e.g., from ZeroCostDL4Mic or the BioImage Model Zoo) in a Jupyter notebook environment.
- Transfer and organize microscopy data on the HPC system to prepare scalable analysis workflows.
- Execute pre-installed bioimage analysis tools (e.g., Ilastik, Fiji, Napari) on the VSC for tasks such as segmentation and denoising.
- Run image analysis pipelines using a Jupyter notebook.
- Adapt existing image analysis pipelines (e.g., from ZeroCostDL4Mic or BioImage Model Zoo) to run efficiently on the HPC infrastructure.
- Evaluate the reproducibility of bioimage analysis workflows and propose improvements using HPC-based solutions.
This course combines short lectures with guided hands-on exercises on the HPC.
This training is recommended for people with no prior experience in HPC who plan to utilize HPC for bioimage analysis tasks.
Notions of command line and scripting, being comfortable with a remote desktop, and general knowledge of image analysis.
This course is part of the learning path Bioimaging.
AI methods used
The course covers machine learning and deep learning methods for large-scale bioimage analysis, including Random Forest for classification, neural networks for segmentation with StarDist, and panoptic segmentation with Empanada.
Trainers
Sebastian Munck
Tatiana Woller
Tatiana Woller is a data expert at the BioImaging Core Leuven and the VIB Data Core.
Her task focuses on exploring and finding solutions for data management of biological images.
Benjamin Pavie
Program
Introduction, HPC Infrastructure, BioImage Analysis
Lunch (provided)
HPC Infrastructure / BioImage Analysis
Short recap, Jupyter notebook & Napari plugins
Wrap up
Lunch (provided) & end of the course
Practical info
18 September 2025 - 19 September 2025
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
18 September 2025 - 19 September 2025
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.
18 September 2025 - 19 September 2025
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).
18 September 2025 - 19 September 2025
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.