How to start with spatial omics?

How to start with spatial omics?

05 December 2023

Ghent - VIB/UGent FSVM II

omics
live training

How to start with spatial omics?

Target Audience:
VIB PhD student
VIB postdoc
VIB staff scientist
VIB group leader or expert
VIB technical support
Location:

Ghent - VIB/UGent FSVM II

Duration:

05/12/2023

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.

Learning outcomes

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...

- testimonies of VIB users of these spatial omics platforms

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 a training later next year.

Trainers

Evelien Van Hamme
VIB Training & Conferences - Trainer picture - Evelien Van Hamme
VIB Spatial Catalyst, BE

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.

Contact Evelien Van Hamme :
Carolin Seyfferth
VIB Training & Conferences - Trainer picture - Carolin Seyfferth
VIB-UGent Center for Plant Systems Biology, BE

After her PhD at the Max Planck Insititut for Plant Breeding Research (Germany) on the transcriptional responses during plant microbe interactions, she went to the Plant Science Center in Umea (Sweden), to study wood development. Since 2020, Carolin is coordinator of the plant single cell platform – a service platform that evaluates novel technologies around single cell omics for plants.

Contact Carolin Seyfferth :
Isabelle Scheyltjens
VIB Training & Conferences - Trainer picture - Isabelle Scheyltjens
VIB-KU Leuven Center for Cancer Biology, BE

 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. 

Contact Isabelle Scheyltjens :
Lars Borm
VIB Stein Aerts Lab, BE

Lars Borm joined VIB as a postdoc in the lab of Stein Aerts. For his PhD he worked on developing new spatial transcriptomics methods. These were used to study the cellular organization of tissues with a focus on the mouse and human (developing) brain. Now he switched organisms to study the cellular architecture of the developing Drosophila melanogaster.

Contact Lars Borm :
Melanie Planque
VIB Spatial Metabolomics Expertise Center, BE

Mélanie Planque is the head of the Spatial Metabolomics Expertise Center at VIB Center for Cancer Biology. After her PhD in proteomics at the University of Namur, she joined the VIB Laboratory of Cellular Metabolism and Metabolic Regulation as a mass spectrometry and metabolomics expert. Since 2023, she works in the Spatial Metabolomics Expertise Center and she collaborates with scientists to support biological, pharmaceutical, and medical fields in their research.

Contact Melanie Planque :

Program

9h30-11h00 overview of platforms, their characteristics, pros and cons

11h00-11h15 break

11h15-12h00 how to get started with spatial omics

12h00-12h30 What can the Single Cell and Spatial Multiomics Expertise Center mean for your research? (Isabelle Scheyltjens)

12h30-13h30 lunch

13h30-14h00 Spatial omics in plants: opportunities, challenges & limitations (Carolin Seyfferth)

14h00-14h30 Mass spectrometry imaging: an emerging tool for studying metabolism (Melanie Planque)

14h30-15h00 Spatial transcriptomics with EEL FISH and application examples on human development (Lars Borm)

15h00-16h00 cookies and informal talks with experienced users

Practical info

Location & Venue

05 December 2023

Ghent - VIB/UGent FSVM II

Technologiepark 75
9052 Zwijnaarde
Belgium

Public transport

05 December 2023

Ghent - VIB/UGent FSVM II
Public transport

From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.

Bike

05 December 2023

Ghent - VIB/UGent FSVM II
Bike

Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
 

Shared bicycles:

Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic

There are also some public bicycle pumps at the park.

Route description

05 December 2023

Ghent - VIB/UGent FSVM II
Parking

Route description

There is only one entrance to Technologiepark. At the entrance, please take a ticket  - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.

Venue contact

05 December 2023

Ghent - VIB/UGent FSVM II
Extra information

room L5 of the FSVM2 building, Technologiepark, Gent

https://cmb.sites.vib.be/en/contact