Bioinformatics Seminars

Bioinformatics Seminar

Time: 11AM
Venue: Teams

3 May 2022

Spatial analysis of high dimensional in situ cytometry data

Ellis Patrick
University of Sydney

Understanding the interplay between different types of cells and their immediate environment is critical for understanding the mechanisms of cells themselves and their function in the context of human diseases. Recent advances in high dimensional in situ cytometry technologies have fundamentally revolutionized our ability to observe these complex cellular relationships providing an unprecedented characterisation of cellular heterogeneity in a tissue environment. This presentation will introduce an analytical framework for analysing data from high dimensional in situ cytometry assays including CODEX, CycIF, IMC and High Definition Spatial Transcriptomics. This framework makes use of functionality from our Bioconductor packages spicyR, listClust, scFeatures, treekoR and ClassifyR. I will provide an overview of the key steps in a spatial analysis pipeline which are needed to interrogate the comprehensive spatial information generated by these exciting new technologies including cell segmentation, feature normalisation, cell type identification, microenvironment characterisation, spatial hypothesis testing and patient classification.

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