Fig. 5: 3D whole cell DNA-PAINT imaging using an SDC-OPR microscope.

a 3D DNA-PAINT image of mitochondrial structures in U2OS cells acquired with an SDC-OPR microscope. Mitochondria were labeled using a DNA-conjugated secondary nanobody targeting a primary antibody against TOM20. Details on sample preparation are provided in the Methods, and imaging conditions are summarized in Supplementary Table 1. Color indicates axial position. A zoomed-in region highlights the mitochondrial network structure. b Differential axial sections from (a) at distinct axial ranges: 0–1.8 µm (top), 1.8–3.6 µm (middle), and 3.6–5.5 µm (bottom). The color scale is consistent with (a). Scale bars = 5 μm. c Cross-sectional views (yz or xz) from individual mitochondria at different axial ranges denoted by white dashed lines in (b). Axial histograms depict mitochondrial membrane distributions, with standard deviations of 30 nm and 42 nm (top), 50 nm and 51 nm (middle), and 51 nm and 65 nm (bottom). Bead calibration using cspline 2D model algorithm is detailed in Supplementary Fig. 10. 3D mitochondria sample imaging was repeated in three independent experiments. Source data of histograms are provided as a Source Data file.