Hands-on introduction to spatial proteomics data analysis
Hands-on introduction to spatial proteomics data analysis
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.
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.
You have to follow the spatial transcriptomics data analysis course first.
Trainers
Arne Defauw
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.
Frank Vernaillen
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.
Julien Mortier
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.
Practical info
25 June 2025
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
25 June 2025
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
25 June 2025
Ghent - VIB/UGent FSVM II
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.
25 June 2025
Ghent - VIB/UGent FSVM II
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.
25 June 2025
Ghent - VIB/UGent FSVM II
room L4 of the FSVM2 building, Technologiepark, Gent