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

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

doi:10.1038/s41467-024-48870-5

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

Nat Commun. 2024 Jun 15;15(1):5135. doi: 10.1038/s41467-024-48870-5.

Authors

Alastair Magness^#¹, Emma Colliver^#², Katey S S Enfield^#², Claudia Lee², Masako Shimato², Emer Daly², David A Moore^{2

3

4}, Monica Sivakumar³, Karishma Valand⁵, Dina Levi⁶, Crispin T Hiley^{2

3}, Philip S Hobson⁶, Febe van Maldegem^{5

7

8

9}, James L Reading^{3

10

11}, Sergio A Quezada^{3

11}, Julian Downward⁵, Erik Sahai¹², Charles Swanton^{13

14

15}, Mihaela Angelova¹⁶

Affiliations

¹ Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK. [email protected].
² Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
³ Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
⁴ Department of Cellular Pathology, University College London Hospitals, London, UK.
⁵ Oncogene Biology Laboratory, The Francis Crick Institute, London, UK.
⁶ Flow Cytometry, The Francis Crick Institute, London, UK.
⁷ Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands.
⁸ Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands.
⁹ Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands.
¹⁰ Pre-cancer Immunology Laboratory, University College London Cancer Institute, London, UK.
¹¹ Immune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research, Department of Haematology, University College London Cancer Institute, London, UK.
¹² Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK.
¹³ Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK. [email protected].
¹⁴ Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. [email protected].
¹⁵ Department of Oncology, University College London Hospitals, London, UK. [email protected].
¹⁶ Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK. [email protected].

^# Contributed equally.

Abstract

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 within tissue compartments, marker positivity calls and spatial metrics such as cellular barrier scores, along with summary graphs and spatial visualisations. PHLEX was developed using imaging mass cytometry (IMC) in the TRACERx study, validated using published Co-detection by indexing (CODEX), IMC and orthogonal data and benchmarked against state-of-the-art approaches. We evaluated its use on different tissue types, tissue fixation conditions, image sizes and antibody panels. As PHLEX is an automated and containerised Nextflow pipeline, manual assessment, programming skills or pathology expertise are not essential. PHLEX offers an end-to-end solution in a growing field of highly multiplexed data and provides clinically relevant insights.

MeSH terms

Animals
Deep Learning*
Humans
Image Cytometry / methods
Image Processing, Computer-Assisted / methods
Mice
Phenotype
Single-Cell Analysis / methods
Software
Spatial Analysis

Abstract

MeSH terms

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