Extended Data Fig. 4: Visualizing complex organelle and cell-surface morphologies.

a, 3D rendering of a neutrophil with organelles labelled. b, Left: Histogram displaying the frequency distribution of LAG3 spots per cell. The x-axis represents the number of LAG3 spots identified within individual cells, and the y-axis indicates the frequency of cells corresponding to each LAG3 spot count. Right: Distribution of LAG3 puncta by cell type. Shown as a boxen plot, where each box represents a quantile range, progressively detailing the distribution from the median outwards to the extremes. Open circles indicate outliers. c, Surface rendering of five interacting immune cells in the MIS, including three CD4⁺ helper T cells (magenta) and two CD8⁺ T cells (cyan). Left: MX1 biomolecular condensates (green), globular GZMB⁺ (yellow) in CD4⁺ T cells. Spacing between opposed membranes is <1.5 µm and contact area is ~20 µm². Scale bars 5 µm. Right: Reversed opacity of left image, showing punctate LAG3 (yellow) on the membranes of CD8⁺ T cells. d, Comparison of GZMB morphology (arrows) within a CD8 and a CD4 T cell in the MIS. e-g, Volumetric renderings showing PD1 and PDL1 can manifest as different morphologies within the same sample (Dataset 3 - LSP22409). e, Diffuse PDL1 on dendritic and CD8⁺ T cells. f, Diffuse PD1 and punctate PDL1 within the same dendritic cell. g, colocalization of punctate PD1 and PDL1 within the same dendritic cells. h, Activated LAG3⁺ GZMB⁺ CD103⁺ PD1⁺ CD8⁺ T cell with long filopodia (red) and dendritic cell (purple) interacting with a tumour cell. Note: This is a different cell community from that in Fig. 2p-r. i, Same cells as (h) with GZMB and LAG3 shown, highlighting that the T cell is activated and cytotoxic. j, surface rendering of interactions in (h) and (i), showing the filopodia in greater detail. k, 3D rendering of cells highlighted in the multicellular interactions in Fig. 3f-g and Supplementary Video 6.