How to start with spatial omics?
How to start with spatial omics?
30 April 2025, 9h30-16h00
General context
This training is a joint effort of VIB Technologies intended for scientists who want to make the leap into the field of spatial omics.
The training will show:
- an overview of the different spatial omics platforms that are available in VIB and a short description of the underlying technology
- a comparison of the characteristics of the platforms to help you decide which platform is best for solving your research question
- info on how to get started with spatial omics: where are the machines, how can you use them, what is the cost of using them, how to prepare your samples, how to select a panel of target genes/proteins...
- guest lectures of VIB scientist on new developments in the field
There will be ample opportunities for discussion and questions to more experienced users. In this way, we hope to start building a spatial omics community in VIB.
Note: Analysis of spatial omics data will not be covered directly, but will be subject of two trainings in June:
Trainers
Evelien Van Hamme
Evelien Van Hamme leads the Spatial Catalyst team in VIB. She obtained her PhD in 2009 at the university of Ghent studying viral entry of coronaviruses in monocytes. She has 12 years of experience in advanced bio imaging applications such as live cell imaging, functional imaging and CLEM workflows. In 2018 her interest in spatial technologies was raised when she started evaluating the Akoya CODEX technology. Since 2023 she focuses on spatial technology applications in life science research together with a team of data analysts.
Isabelle Scheyltjens
Isabelle did a PhD in the KULeuven lab of Neuroplasticity and Neuroproteomics. To learn more about single cell technologies, she started a Postdoc in the VIB-VUB lab of Myeloid Cell Immunology where she performed the wetlab and analysis of scRNA-Seq on mouse models for Alzheimers Disease, in collaboration with Janssen Pharmaceutica.
Since May 2022, she started a new position in the VIB-KULeuven Center for Cancer Biology (CCB) to dive deeper into the spatial dimension. She became part of the new Single Cell & Spatial Multiomics expertise center to develop, optimize and implement novel spatial and high-plex -omics technologies.
Kristofer Davie
Bioinformatician with over 8 years of experience in the analysis of a wide variety of next generation sequencing data types, with a strong focus on the analysis of single cell data (sc/snRNA-seq, scATAC-seq, Spatial technologies).
Marco Giampà
In the Metabolomics Core, Marco serves as the MSI specialist. He is integrating spatial dimensions into tracer metabolomics workflows. His expertise is key in developing and implementing novel methodologies to enhance the resolution, accuracy, and clinical relevance of metabolomics research.
Program
9h30-10h00 Introduction to spatial omics
10h00-10h40 Getting Started with Mass Spectrometry Imaging for Metabolomics Research (Marco Giampa)
10h40-10h50 Break
10h50-11h50 Overview of platforms, their characteristics, pros and cons
11h50-12h00 Break
12h00-12h40 How to get started with spatial omics
12h40-13h40 Lunch
13h40-14h20 "Nova-ST: Nano-Patterned Ultra-Dense platform for spatial transcriptomics" (Kristofer Davie)
14h20-15h00 Guest lecture on spatial multi-omics (Isabelle Scheyltjens)
15h00-16h00 Cookies and informal talks with experienced users
Practical info
30 April 2025
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
30 April 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.
30 April 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).
30 April 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.
30 April 2025
Leuven - Campus Gasthuisberg
O&N5 auditorium 4th floor