Bioimaging data analysis on the HPC
10 October 2024
General context
This course will introduce the use/potential of scientific high-performance computing for image analysis. Scientific high-performance computing enables to scale up bioimage analysis and opens new avenues for research. You will learn how to use and access existing supercomputer infrastructures in Belgium (VSC) using the Open On Demand portal. You will learn how to run common image analysis tasks using software with GUI (napari) or through jupyter notebook.You will identify which online and reusable resources are available for your problem (i.e., bioimage model zoo or other resources).
General Learning Outcome:
1- Understand the scientific high-performance computing(HPC) infrastructure
2- Learn to access to the supercomputer infrastructures in Flanders (VSC)
3- Transfert, store bioimage/microscopy dataset on the VSC
4- Find and load modules available on the VSC to analyze the bioimage/microscopy dataset
BioImaging Learning Outcome:
1- Understand the benefit of using the HPC/VSC infrastructure to analyze bioimage/microscopy dataset
2- Run pre-installed solution on the HPC/VSC (Ilastik/Fiji/Napar...) for bioimage analysis tasks (segmentation, denoising etc...)
3- Run image analysis pipeline using a jupyter notebook
4- Adapting existing solution (zerocost, bioimage zoo) on the VSC
5- Discuss how to improve reproducibility in image analysis
This training is recommended for people with no experience in HPC who are planning to use the HPC for bioimage analysis tasks.
- Have notions of command line and scripting
- Be comfortable working with remote desktop
To follow the course more easily, we expect general knowledge of image data analysis.
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
9h30 - Introduction
10h00 - HPC infrastucture
10h30 - Coffee Break
10h45 - Data Transfer
11h15 - Napari
12h15 - Lunch
13h15 - Napari plugins
14h30 - Coffee break
14h45 - Jupyter notebooks
17h00 - End of the day
Practical info
10 October 2024
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
10 October 2024
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.
10 October 2024
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).
10 October 2024
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.
10 October 2024
Leuven - Campus Gasthuisberg
O&N 5 - 4th floor - room 04.343