Hands-on introduction to targeted spatial transcriptomics data analysis
Hands-on introduction to targeted spatial transcriptomics data analysis
23 June 2025, 9h30-17h00
24 June 2025, 9h30-17h00
General context
In recent years, spatial transcriptomics technologies have become increasingly accessible to researchers with the emergence of a wide array of commercially available targeted and untargeted approaches. While these technologies offer tantalizing opportunities to study extensive gene panels in their spatial context, the resulting data are often complex, and answering research questions of interest requires a thorough understanding of spatial data analysis and the use of dedicated tools. To this end, this training will present a hands-on introduction to the analysis of targeted spatial transcriptomics data using the SPArrOW/Harpy pipeline developed by the Yvan Saeys group (VIB).
In this course, we will teach you how to run the Harpy pipeline for targeted spatial transcriptomics data (i.e., imaging-based technologies such as Xenium (10X Genomics), MERSCOPE (Vizgen), Molecular Cartography (Resolve Biosciences), ...). Specifically, the following topics will be covered:
- How to read in the data outputted by the commercial vendors.
- How to optimize segmentation and allocate the transcripts to cells.
- How to cluster the data and create UMAPs.
- How to run the analysis on an HPC.
Those who want to know more about the practical side of spatial omics experiments and who want a comprehensive overview of the different spatial platforms should attend the How to start with spatial omics workshop.
Participants should have some experience with Linux and running jobs using the HPC/VSC. For those who lack these skills, we organize a free Linux session and a free HPC session on Friday, June 20th, in Ghent.
Participants should also have some experience with Python. For those who have no experience at all with Python, we recommend to follow the Light 1 day Python introduction session (where you will learn to understand Python code as used in the spatial data analysis training and adjust it to your needs).
The spatial data analysis course will use Jupyter notebooks, conda environments, pandas DataFrames, numpy arrays and Matplotlib visualizations. If you lack these skills you should follow the free Python for spatial data analysis course on Friday, June 13th, in Ghent.
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
23 June 2025 - 24 June 2025
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
23 June 2025 - 24 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.
23 June 2025 - 24 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.
23 June 2025 - 24 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.
23 June 2025 - 24 June 2025
Ghent - VIB/UGent FSVM II
room L4 of the FSVM2 building, Technologiepark, Gent