Fig. 2: CISA robustly characterizes protein localization at cell-cell interfaces from IMC data.

a Density plots showing correlation of σ(CD4) with σ(CD3) in CD8+ cells, and correlation of σ(CD8a) with σ(CD3) in CD8+ cells; (b) correlation of σ(CD4) with σ(CD3) in CD4+ cells, and correlation of σ(CD8a) with σ(CD3) in CD4+ cells. c Comparison of CD8/CD3 correlation in CD8+ cells at the pixel level to CISA. d Comparison of CD4/CD3 correlation in CD4+ cells to CISA. e–h Plots are analogous to (a–d) but for melanoma IMC data from (Hoch et al. 2022). Examples of positive (i) and negative (j) localization of CD3 and CD8a around the central T cell (dashed cell boundary) toward neighboring macrophages (solid white cell boundary). The “Combined” column shows the four channels listed as separate columns with corresponding colors, plus blue showing DNA. In the “Cell type” column, green marks macrophages and red marks T cells. In the CD3 and CD8a columns, numbers indicate synapse strengths of the shown marker between the central T cell and the indicated macrophage. Gray outlines: non-contacting or non-APC cells. Scale bar: 10 µm. k Correlations of σ(CD4), σ(CD8a) σ(CD7) and σ(ICOS) with σ(CD3) in CD4 + T cells. Each point is one TMA core. l Correlations of σ(CD4), σ(CD8a) σ(CD7) and σ(ICOS) with σ(CD3) in CD8 + T cells. m Average pixel intensity of markers within CD8 + T cells. ICOS (CD278), is significantly lower than CD4. Each point is the average in a TMA core. a–d, i, j are based on melanoma IMC spots from the (Moldoveanu et al. 2022)²⁴ IMC dataset. e–h, k–m data are from the (Hoch et al. 2022)²³ IMC data. Tc: CD8 + T cells; Th: CD4 + T cells. σ: interface-level synapse strength.