Workshops and courses

ELIXIR node event Spatial proteomics data analysis

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Date: No date given

Language of instruction: English

Imaging-based spatial proteomics technologies are increasingly used to study tissue organization and protein expression within spatial contexts. These methods enable high-dimensional characterization of proteins across tissue sections using platforms such as MACSima (Miltenyi Biotec), COMET (Lunaphore), and PhenoCycler Fusion (Akoya Biosciences). However, handling and analyzing the resulting data can be challenging, requiring specialized workflows. This course serves as a follow-up to the Targeted spatial transcriptomics analysis training and focuses on the Harpy pipeline for spatial proteomics analysis. This includes cell segmentation, feature extraction, and unsupervised clustering of cells or pixels to support cell-type annotation. You will learn to process, visualize, and interpret data from multiplex imaging platforms efficiently and reproducibly. 

Keywords: advanced bioinformatics, Artificial Inteligence, omics

Learning objectives:

  • “Annotate cell populations using the Harpy pipeline”
  • “Import and structure imaging-based spatial proteomics data from different commercial platforms”
  • “Optimize segmentation strategies for multiplex imaging datasets”
  • “Quantify marker expression levels in a spatial context”

Organizer: VIB

Event types:

  • Workshops and courses

Sponsors: Vlaams Supercomputer Centrum

Instructors: Arne Defauw, Frank Vernaillen, Julien Mortier

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