Revealing cellular niches and spatial interactions in heterogeneous spatial omics data

CellCharter: flexible and scalable spatial cell niches

CellCharter is an algorithmic framework to study communities of cells within tissues. Its main objective is to reveal how distinct types of cells operate and function in targeted areas. This offers deeper insights into cellular behaviour and interactions within diverse biological environments, including cancer.  CellCharter surpasses existing methods by not only identifying biologically relevant cellular niches in different contexts but also by revealing distinct spatial cancer cell states. 

 

In this video, you will also see how you can use CellCharter to detect artifacts from immunofluorescence data. 

 

If you are a cancer biologist, developmental biologist or a neuroscientist interested in cell communities, then this talk is for you! 

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Speaker
Name:
Marco Varrone
Institute:
University of Lausanne
Group:

Marco Varrone is a PhD student in the Computational Systems Oncology lab at the University of Lausanne. He obtained an MSc degree in Computer Science and Engineering at Politecnico di Milano, Italy. During his master's thesis project, he worked on studying the relationship between gene expression and chromatin structure. He is now working on characterizing intra-tumor heterogeneity through the computational analysis of spatial omics data.

Video
Duration:
9 minutes 30 seconds
License:

This video is available under the creative commons license CC-BY-4.0

Reference(s)

Varrone M, Tavernari, D., Santamaria-Martínez, A. et al. CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity. Nat Genet 56, 74–84 (2024).

DOI:
10.1038/s41588-023-01588-4

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