Fig. 2: Multiplexed imaging and cytometry of Z-tag-labeled breast epithelial cell lines.
From: Multielement Z-tag imaging by X-ray fluorescence microscopy for next-generation multiplex imaging
a–m, MEZ-XRF imaging of the markers indicated by element and emission line and antigen symbol (rows) in four breast epithelial cell lines (columns): In_Ka|HH3 (a); Eu_Ka|HH3 (b); Yb_L3|HH3 (c); I_Ka|IdU (d); Y_Ka|pHH3 (e); Ce_Ka|pHH3 (f); Tm_L3|EGFR (g); Tb_Ka|HER2 (h); La_Ka|CK8/18 (i); Pr_Ka|CK5 (j); Nd_Ka|CD44 (k); Gd_Ka|Vim (l) and Ag_Ka|Tissue (m). Each column shows the same field of view imaged with a 500 nm focused 69 keV X-ray beam with 500 nm raster steps at 1 Hz. XRF emissions were recorded with an SDD. n, Cell (upper panels) and nuclear (lower panels) segmentation masks generated with Mesmer for the four epithelial cell lines. o, Pearson correlation heatmap of single-cell intensities of the indicated markers. Labels indicate element emission lines and marker. p, Leiden clustering on single-cell intensities of an informative marker (one per cell type), plus Ce-pHH3 and I-IdU. q, Cell masks colored by Leiden clusters identified in p. r, Heatmap of single-cell expression patterns ordered according to the Leiden clusters identified in p. s, Relative nuclear to nonnuclear intensities for the indicated markers. Markers above axis bars are nuclear, below axis bars are nonnuclear. Violin plots (three dashed horizontal lines per violin show the lower quartile, median value and upper quartile values) show distribution of nuclear/nonnuclear marker ratios for all cells of a single field of view for one sample per cell type. t, Signal-to-noise comparison between MEZ-XRF with SDD. The data for the same samples imaged by IMC are shown in Extended Data Fig. 4.
