Pre-FIB Layer-Mapping Cryo Tomography (PLCT) for Depth-Resolved in Situ Structural Analysis of Multilayered Tissues

Cryo-electron tomography (cryo-ET) enables near-native visualization of subcellular architectures, yet applying it to moderately thick, multilayered tissues such as the retina is hampered by inadequate vitrification and inaccurate depth-targeting. Here, we developed PLCT, an integrated approach combining modified high-pressure freezing, cryo-ultramicrotome trimming, and plasma-based cryo-FIB milling to overcome these barriers. PLCT reliably vitrified <100 m retinal strips with minimal ice artifacts, navigates precisely to the outer plexiform layer using morphological landmarks, and produces high-quality lamellae suitable for high-resolution cryo-ET. Subtomogram averaging (STA) analysis identified microtubules at 16.33 [A] within retinal horizontal cell processes. Importantly, STA also resolved a 10-nm-diameter filamentous structure at 24.81 [A] in the same processes, featuring six peripheral strands surrounding an elongated central density with continuous intervening cavities, an architecture consistent with intermediate filaments. Together with its native localization and immunoreactivity, these features collectively identify the filaments as neurofilaments. Separately, 3D reconstruction of synaptic ribbons uncovered a previously unrecognized "mahjong tile"-like fine ultrastructure. These results demonstrate that PLCT-produced lamellae are of sufficient quality to support structural analysis in native tissue. Although demonstrated on retinal photoreceptor synapses as a proof-of-principle, PLCT is inherently generalizable, with its depth-navigation and vitrification strategies directly applicable to any multilayered tissues. This work establishes PLCT as a robust, reproducible platform for depth-resolved in situ cryo-ET of multilayered tissues.