The detection efficiency of low-dose cryo-4D STEM for biogenic crystals in frozen-hydrated samples

Multimodal scanning transmission electron microscopy on vitrified frozen-hydrated specimens promises exceptional spatial resolution into the molecular mechanisms underlying the formation of organic crystals in both health and disease. Detection of crystalline volumes is essential for tracking and mapping nucleation and growth. We provide an analytical description of the low-dose detection limit in diffraction for a thin crystal embedded in a thick matrix, focusing on organic crystals and embedding matrices of low-Z elements such as vitrified ice. Numerical calculations refine our description by accounting for the effects of multiple scattering. Often underestimated, wide-angle tails associated with inelastic scattering play a crucial role for the detection of crystalline reflections in a thick ice matrix, common for cryo-electron microscopy. We show that guanine crystals as thin as a few nanometers can be detected with a fluence of just a few thousand electrons if the ice thickness is below one mean free path for inelastic scattering. The required fluence increases non-linearly with the embedding ice thickness, with a pronounced top-bottom effect regarding the location of the crystal in the sample. Energy-filtered recording significantly reduces the fluence needed for thicker samples. The low-dose simulations implemented here validate the analytical description while acknowledging its limitations due to abstraction from multiple scattering and beam spreading.