Extended Data Fig. 6: MEZ-XRF and matched IMC images of additional markers in breast cancer samples.

a-j, Matched MEZ-XRF (left) and IMC (right) overviews (top) and ROIs (bottom). Samples are presented in columns and element/marker channels in rows. MEZ-XRF labels indicate element_emission lines/marker (as in Fig. 2a–m). IMC labels indicate isotope/marker (as in Extended Data Fig. 5). Blue arrows indicate SMA⁺ vasculature, yellow arrows indicate PR⁺ cells identified in both MEZ-XRF and IMC images. MEZ-XRF overviews were imaged with a 500-nm diameter spot focused X-ray beam with 2-µm raster steps at 20 Hz. MEZ-XRF ROIs were imaged with a 500-nm diameter spot focused X-ray beam with 500-nm raster step at 5 Hz. MEZ-XRF images are 0.5—99.5% grey levels of detector counts per element emission line matched across samples as shown in colour bars. IMC images were scanned once after MEZ-XRF using a 500-nm step (pixel size) with raster ablation at 200 Hz. Overview scans were down sampled 1:4 to match the 2-µm step sampling used for MEZ-XRF overviews. IMC images are 0.5–99.5% grey levels of IMC counts per isotope matched across samples as shown in colour bars.