Fig. 3

Quantification of immune cell densities in stroma and tumour areas of sq-BLCA. A Visualization of the computer-based analysis: (i) TMA Core stained for CD3 and (ii) detail magnification with tumour and stroma areas. (iii + iv) Positive cell detection by QuPath highlighting positively stained cells in red and non-stained cells in blue edging. (v + vi) Classifier categorizing pixels into tumour (red) and stroma (green), allowing subsequent allocation of positively stained immune cells in intratumoural and stromal TILs; Black scale bar (i, iii, v): 250 µM; Black scale bar (ii, iv, vi): 50 µM. (B-H) Immune cell density quantified by QuPath in iTILs and sTILs for CD3 + (B), CD4 + (C), CD8 + (D), CD79A + (E), CD68 + (F), CD163 + (G) and neutrophils (H). I Pairwise heatmap visualization demonstrates a strong correlation for the presence of T-cells (CD3, CD4 and CD8) as well as macrophages (CD68 and CD163); ns: not significant; ***p < 0.001