Normalized basis patterns in 2-D (lateral dimensions) are shown in Figure 4 with 8 bit intensity resolution for axial dimension at the nominal focus.
Dipole orientations containing larger contributions from Ixz and Iyz will be inherently more sensitive to dipole axial position since these patterns have a larger "intensity" gradient in the axial dimension near the nominal focus.
Light is scattered within the sample, both from regions in the nominal focus and regions outside of focus.
Spaced a distance from the aberrator, at the nominal focus of the objective, we chose to use a polished, uniformly reflecting piece of glass as the object surface.
Cryo-EM images were collected at a nominal magnification of 29000× and pixel size of 1.21 Å with a nominal focus range from 2.5 5.0 µm under focus.
The pinhole acts as a spatial filter to increase the average signal-to-background ratio for light that scatters near the nominal focus [ 1, 2].
We note that the FPP model only considers pupil aberration experienced by the ballistic and quasi-ballistic light as it proceeds to the nominal focus.
Images were collected at a nominal magnification of 62,000× and a pixel size of 1.36 Å with a dose of ∼30 e-/Å and a nominal focus range from 0.8 1.8 µm under focus.
An aberrator can be associated with those aberrations that affect both the light that reaches the nominal focus at z d and that returns for collection by the objective.
The background field, U B, is caused by light that is scattered within the tissue, from outside the nominal focus, but due to the re-direction of multiple scattering, is collected by the objective and focused to the pinhole.
Images were collected at a nominal magnification of 52000× and pixel size of 2.05 Å with a dose of ∼30 e-/Å and a nominal focus range from 0.8 1.8 µm under focus.
