TRACERx-PHLEX is a user-friendly pipeline for end-to-end analysis of multiplex imaging data. See the detailed tutorial for running TRACERx-PHLEX with available options, guidelines and troubleshoothing.
It implements and automates the following integral steps for multiplexed imaging analysis:
- segments nuclear and cell objects (deep-imcyto)
- automatically identifies and annotates cell types and cell states (TYPEx)
- segments tissue compartments such as tumour and stroma (TYPEx)
- performs a range of spatial analyses (Spatial-PHLEX)
These steps are implemented as individual modules that can be run independently or as an uninterrupted fully automated end-to-end workflow (Quick start).