Hands-on introduction to spatial proteomics data analysis

Hands-on introduction to spatial proteomics data analysis

25 June 2025

Ghent - VIB/UGent FSVM II

advanced bioinformatics
omics
live training

Hands-on introduction to spatial proteomics data analysis

Target Audience:
VIB PhD student
VIB postdoc
VIB staff scientist
VIB group leader or expert
VIB technical support
Flemish academic or researcher
Non-Flemish academic or researcher
Industry professional
Location:

Ghent - VIB/UGent FSVM II

Duration:

25 June 2025, 09h30 - 17h00

General context

This course is a follow up session on Hands-on introduction to targeted spatial transcriptomics data analysis, where the Harpy pipeline for spatial proteomics is explained.

Learning outcomes

In this course, we will teach you how to use the Harpy pipeline for imaging-based spatial proteomics data, e.g., MACSima (Miltenyi Biotec), COMET (Lunaphore), PhenoCycler Fusion (Akoya Biosciences), Opal (Akoya Biosciences), ... 

Specifically, we will cover the following topics:

  • How to read in the data outputted by the commercial vendors.
  • How to optimize segmentation for multiplex imaging.
  • How to quantify marker expression.
  • How to annotate cell types.
Required skills

You have to follow the spatial transcriptomics data analysis course first.

Trainers

Arne Defauw
VIB Spatial Catalyst, BE

Arne holds a masters degree in Mathematics and a PhD in Physics. After his PhD he worked as a machine learning engineer in the industry, where he specialized in natural language processing. Now he works at VIB Spatial Catalyst, where he contributed to SPArrOW, a python library to analyse all types of spatial transcriptomics data. As a member of the Spatial Catalyst he also provides support for spatial omics data analysis and helps optimize bioinformatic tools for spatial analysis.

Contact Arne Defauw :
Frank Vernaillen
Frank Vernaillen
VIB Spatial Catalyst, BE

After working as a software developer in a company on physics-based modeling and 2D and 3D computer graphics, Frank joined VIB in 2016 to work on image restauration and registration of electron microscopy images, machine learning,... Via VIB's first imaging-based spatial proteomics platform, he got involved in spatial omics data analysis, and naturally joined the Spatial Catalyst when it was formed in 2023, to continue work on data analysis and development of analysis pipelines.

Contact Frank Vernaillen :
Julien Mortier
Julien Mortier
VIB Spatial Catalyst, BE

Julien obtained his PhD on phenotypic heterogeneity and stress responses in bacteria. In his postdoc at SciLifeLab, he developed a machine-learning based image analysis workflow to study phenotypes of bacteria under starvation conditions and he established an end-to-end workflow for Transposon Sequencing. Now he works at VIB Spatial Catalyst, where he provides support for spatial omics data analysis and helps optimize bioinformatic tools for spatial analysis.

Contact Julien Mortier :

Practical info

Location & Venue

25 June 2025

Ghent - VIB/UGent FSVM II

Technologiepark 75
9052 Zwijnaarde
Belgium

Public transport

25 June 2025

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

25 June 2025

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

25 June 2025

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

25 June 2025

Ghent - VIB/UGent FSVM II
Extra information

room L4 of the FSVM2 building, Technologiepark, Gent

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