How to start with spatial omics?

How to start with spatial omics?

21 April 2023

Ghent

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

Duration:

21 April 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 this 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 :
Birthe Haest
VIB-UGent Center for Inflammation Research, BE

Birthe Haest is a PhD student in the laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration of Prof Martin Guilliams at Flanders Institute for Biotechnology (VIB)-UGent Center for Inflammation Research. In 2019, she obtained her Master degree in Biochemistry and Biotechnology at Ghent University. For her master’s thesis she went to Maynooth, Ireland, to study macrophage activation. In 2022, the proteogenomic atlas of human and murine liver was published in Cell. This was a huge collaborative effort between the Guilliams and Scott labs in which Birthe took part. Currently, she is investigating the cell-cell interactions that drive liver regeneration.

Bart Ghesquière
VIB Metabolomics Core Leuven, BE

Group leader

Hilde Nelissen
VIB-UGent Center for Plant Systems Biology, BE

My research career has focused on the central biological question: How do growth processes determine final plant organ size? Initially, I approached this using molecular biology studying Arabidopsis leaf development. As my interest shifted towards applied research, I redirected my focus to maize. What started as translational research to bring knowledge from Arabidopsis to crops and from the lab to the field, gradually developed into a research line with the goal to decipher the instructor networks that govern leaf size, organ growth and ultimately yield in maize. Because plant organ size control is an important yield component that is also severely impacted by climate change, our ultimate goal is to deepen our understanding of the growth-regulatory networks to enhance our success rate to achieve climate-resilient crops.
Group leader @ Systems Biology of Yield, VIB - PSB

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 to consider specifically for plant samples

12h30-13h30 lunch

13h30-14h00 how to design gene/protein panels

14h00-14h30 how to start with spatial metabolomics

14h30-15h30 cookies and informal talks with experienced users

15h30-16h00 Q&A session and conclusion

Practical info

Location & Venue

21 April 2023

Ghent - VIB/UGent FSVM II

Technologiepark 75
9052 Zwijnaarde
Belgium

Public transport

21 April 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

21 April 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

21 April 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

21 April 2023

Ghent - VIB/UGent FSVM II