Fig. 4: Example image outputs from TYPEx in the TRACERx 100 IMC dataset.
From: Deep cell phenotyping and spatial analysis of multiplexed imaging with TRACERx-PHLEX
TYPEx outputs various images for the user, examples of which are shown for two cases from the PHLEX test dataset (T cells & Stroma panel), including: a A map of cell objects coloured by cell subtype for each analysed sample. b, c For each major cell lineage marker, the samples with the highest cell counts are selected for visual inspection. The positive cell objects for a corresponding marker are overlaid onto a raw single-channel intensity image (b). Each cell object is visualised with a different colour. A raw single-channel intensity image for the markers in major cell lineage definitions is also provided (c). d Tissue segmentation masks based on tumour- and stroma-specific markers. The cell maps and overlays in a, b are generated when the mask of segmented cell objects is provided as input for TYPEx. Scatter plots of annotated cell objects are output as an alternative. LUAD lung adenocarcinoma, LUSC lung squamous cell carcinoma.
