Fig. 3: Correlative light and electron imaging of A. thaliana roots.

Spinning-disk fluorescence (A) and transmission electron microscopy (B) imaging of roots on 500 nm and 70 nm sections, respectively. Composite (panorama) image of individual EM fields of view to capture an overview of a large area of the root (B). Insets, highlighted by red rectangles in the panels (A) and (B), magnified in (C) and (D), showcasing cells of interest (1–4) in the differentiation zone of the root, with anatomical features of the root used for cell identification highlighted by red circles. Anisotropic sample stretching is shown in an overlay CLEM image (E, confocal image thresholded to highlight cell walls). Arrows highlight the problems with image registration, shown on cell wall architecture (notice the mismatch of cell wall contours at the bottom and good fitting at top of the image). Anisotropic stretching shown in the displacement of the fluorescence signal from nuclei (F), not fitting the underlying cell localization observed in TEM data. Detailed view of a root nucleus shown in SMLM reconstruction (G). Details of the same cell in the corresponding EM image (H) and image overlay shown in (I). TL transmitted light, FLUO fluorescence, EZ elongation zone, DZ differentiation zone, RT root tip, Nuc nucleus, No nucleolus, IRF intranucleolar replication focus. Consecutive-section CLEM was perfomed in five biological replicates. Scale bar (A, B): 50 µm, (C–E): 5 µm, (F–I): 2 µm.