Ultra-High Resolution 3D Imaging of Whole Cells

Fluorescence nanoscopy, or super-resolution microscopy, has become an important tool in cell biological research. However, because of its usually inferior resolution in the depth direction (50–80 nm) and rapidly deteriorating resolution in thick samples, its practical biological application has been effectively limited to two dimensions and thin samples. Here, we present the development of whole-cell 4Pi single-molecule switching nanoscopy (W-4PiSMSN), an optical nanoscope that allows imaging of three-dimensional (3D) structures at 10- to 20-nm resolution throughout entire mammalian cells. We demonstrate the wide applicability of W-4PiSMSN across diverse research fields by imaging complex molecular architectures ranging from bacteriophages to nuclear pores, cilia, and synaptonemal complexes in large 3D cellular volumes. [Display omitted] •Whole-cell 4Pi single-molecule switching nanoscopy allows 10- to 20-nm 3D resolution•Refined hardware and new data analysis allow imaging of cells as thick as ∼10 μm•Using structure-averaging, the 3D shape of a bacteriophage can be resolved•Wide applicability across diverse research fields is demonstrated A new super-resolution microscope opens a window deep into cells to image organelles and subcellular structures spanning large volumes.