Ghost Neuron preparation unlocks high-resolution structural mapping of intracellular architecture in axons

Cellular cryo-electron microscopy (cryo-EM) offers powerful tools to reveal molecular architecture inside cells, but dense cytoplasm often obscures fine molecular features, especially in narrow neuronal projections. Here, we introduce the Ghost Neuron technique, a preparation combining brief hypotonic treatment with controlled mechanical rupture immediately before freezing, facilitating high-contrast imaging of neuronal ultrastructure within its neurite topology. By removing the plasma membrane and reducing cytoplasmic density, the method allows high-resolution structural analysis while preserving the overall geometry of neurites. The method allows structural information to be mapped back onto neuronal architecture. The preparation also releases endogeneous macromolecular complexes onto EM grids, creating particle-rich regions suitable for high-resolution structural analysis. Using Ghost Neuron, we resolved axonal microtubules at 3.59 Å and 3.9 Å resolution, distinguishing expanded and compact lattice states, and mapped these states as interspersed patches along individual microtubules within axons. We also resolved axonal actin filaments and identified cofilin-decorated actin. These results establish Ghost Neuron as a discovery platform for linking molecular structure to neuronal organization.