Spatial data analysis
24/06/2024
General context
This training will give an overview of spatial data analysis for a variety of targeted and untargeted spatial omics approaches. The training aims to provide early-career researchers an entry point into spatial data analysis and to give experienced users the opportunity to broaden their knowledge.
In a series of presentations, we will give an overview of the available tools for targeted transcriptomics and proteomics, untargeted transcriptomics, visualization, annotation and downstream spatial analyses such as neighborhood analysis, spatial enrichment, cell-cell interactions... The SPArrOW pipeline, developed by the Yvan Saeys group (VIB) for the analysis of spatial transcriptomics data, will be introduced. After each section, discussion and the exchange of expertise among attendants will be encouraged.
To this end, the training will give an overview of:
- the different analysis methods and tools that are typically being used
- the possible pitfalls during the analysis
- recommendations for experimental design
- who to contact to get assistance with the analysis of your spatial data
The training is intended for everyone in VIB who has generated spatial data or is planning to generate data in the near future and wants a broad overview on what is currently possible during spatial data analysis.
Those who are new to the field are advised to follow an online "How to start with spatial omics" training first (details will be communicated later).
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.
Program
9h30-10h15 Introduction
10h15-10h30 break
10h30-11h45 Targeted transcriptomics and the SPArrOW analysis pipeline
11h45-12h15 Tools for visualization
12h15-13h00 lunch
13h00-14h15 Analysis of spatial proteomics data
14h15-14h30 break
14h30-15h15 Analysis of untargeted transcriptomics data
15h15-16h00 Downstream spatial analysis
Practical info
24 June 2024
Leuven - Park Inn by Radisson
Martelarenlaan 36
3010 Leuven
Belgium
24 June 2024
Leuven - Park Inn by Radisson
The hotel is located 300m from Leuven Central Station, just a short 5 minute walk.
24 June 2024
Leuven - Park Inn by Radisson
Using your bike for longer distances? Check Cycle Highways.
24 June 2024
Leuven - Park Inn by Radisson
Underground P1-Parking Station Leuven, Martelarenlaan 4, 3010 Leuven or parking De Bond, Martelarenlaan 18, 3010 Leuven.
24 June 2024
Leuven - Park Inn by Radisson
+32 16 61 66 02
sales.leuven@parkinn.com