TRACERx-PHLEX: One-stop pipeline for robust multiplexed imaging analyses

TRACERx-PHLEX is a user-friendly pipeline for an end-to-end analysis of multiplex imaging data.

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Citations

The pipeline is described in [Journal X](https://biorxiv.org).

Introduction

TRACERx-PHLEX is a modular pipeline for comprehensive analysis of the tumour microenvironment using multiplex imaging.

Check out the Quick start section for further information, including installation for how to get started with TRACERx-PHLEX.

TRACERx-PHLEX contains three submodules:

PHLEX: deep-imcyto

A module devoted to performing accurate nuclear and cellular segmentation and single cell measurement in multiplex images.

PHLEX: TYPEx

A module for cellular phenotyping from marker expression intensities derived from multiplex images.

Spatial-PHLEX

A module for performing several types of automated spatial analysis.