Targeted spatial transcriptomics analysis
Date: No date given
Duration: P1DT16H
Language of instruction: English
Spatial transcriptomics technologies have become widely used to study gene expression in its spatial context, providing valuable insights into tissue organization. However, the complexity of these datasets requires dedicated analysis methods and tools for reliable interpretation. This training offers a hands-on introduction to analyzing targeted spatial transcriptomics data using the SPARROW/Harpy pipeline, developed by the Yvan Saeys group (VIB). Through practical exercises, you will learn essential steps such as image processing, cell segmentation, transcript assignment, dimensionally reduction, and clustering to study spatial patters effectively. This training is highly practical, combining brief theoretical introductions with hands-on exercises working with real datasets.
Keywords: advanced bioinformatics, Artificial Inteligence, omics
Learning objectives:
- “Apply segmentation techniques to accurately identify cells and assign transcripts within spatial images”
- “Import targeted spatial transcriptomics datasets from commercial platforms (Xenium) into the Harpy pipeline”
- “Interpret clustering and visualization results to draw biologically relevant conclusions from spatial data”
- “Optimize pipeline parameters to improve the quality of segmentation and transcript assignment”
- “Perform clustering and dimensionality reduction (UMAP) to explore spatial patterns”
Organizer: VIB (https://ror.org/03xrhmk39)
Event types:
- Workshops and courses
Sponsors: Vlaams Supercomputer Centrum
Instructors: 
Arne Defauw, Frank Vernaillen, Julien Mortier
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