Fig. 2: Co-detection by indexing (CODEX) multiplex imaging of a reference papilla tissue sample. | Nature Communications

Fig. 2: Co-detection by indexing (CODEX) multiplex imaging of a reference papilla tissue sample.

From: A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

Fig. 2

a H&E stained section that underwent CODEX imaging showing characteristic papillary morphology. b CODEX multiplex imaging displaying 6 markers (CD31- endothelial cells; Cadherin-1 (CDH1)- in papilla marks collecting ducts; CD45- pan immune marker; THY1 (also known as CD90)- marks pericytes; IGFBP7- Injury marker and DAPI- labels nuclei). c Unsupervised clustering and dimensionality reduction of the CODEX data in a t-stochastic neighborhood embedding (t-SNE) plot showing various cells classes, which were validated by the level of fluorescence intensity (heatmap in (d) and examining levels of fluorescence in (f)) and mapping back on the image (example in (e) for CD cells and more details also in Supplementary Figs. 7 and 8). e localization of CD-1, CD-2 and undifferentiated cells (Undiff.) in CODEX images using colored nuclear overlays. f shows the corresponding staining of various markers that characterized the profile of CD-1, CD-2 and Undiff. cells with the corresponding distribution of fluorescence intensity for these markers. CD-2 cells express higher levels of injury markers but are not segregated into separate tubules. Undifferentiated cells are localized to interstitium. g Re-clustering of interstitial cells based on specific markers h in CODEX data identifies populations of fibroblasts (2 subtypes, FIB1 and FIB2) and myofibroblasts (Myo), which were mapped into the interstitium as shown in panel i for each marker. Scale bars: (0.5 mm in a, b, 0.1 mm in e/f and 0.02 mm in (i)). Other abbreviations listed: Endo = endothelial cells; LYM = lymphocytes; Th. Limbs = thin limbs.

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