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Article

Deep cell phenotyping and spatial analysis of multiplexed imaging with TRACERx-PHLEX.

Nature communications - 15 Jun 2024

Magness Alastair, Colliver Emma, Enfield Katey S S, Lee Claudia, Shimato Masako, Daly Emer, Moore David A, Sivakumar Monica, Valand Karishma, Levi Dina, Hiley Crispin T, Hobson Philip S, van Maldegem Febe, Reading James L, Quezada Sergio A, Downward Julian, Sahai Erik, Swanton Charles, Angelova Mihaela

Abstract excerpt

The growing scale and dimensionality of multiplexed imaging require reproducible and comprehensive yet user-friendly computational pipelines. TRACERx-PHLEX performs deep learning-based cell segmentation (deep-imcyto), automated cell-type annotation (TYPEx) and interpretable spatial analysis (Spatial-PHLEX) as three independent but interoperable modules. PHLEX generates single-cell identities, cell densities...

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Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

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Identifiers

PMID: 38879602
DOI: 10.1038/s41467-024-48870-5
PMCID: PMC11180132

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