The microscope settings significantly affect contrast transfer and can induce meaningless artifacts into the pattern of actual structures.
CTF patterns are very sensitive to defocus of objective lens. Ratio of CTFs taken in different defoci oscillates as shown in Figure 1711. The slight difference in defocus causes the contrast transfer functions to fall out of phase, resulting in peaks and dips to appear in the ratio. Therefore, a series of CTF images taken at different defoci in a constant focus step is normally acquired so that the best focus match is found by comparing the Fourier spectra of the images. The way to find the best match is to find the image from which the Fourier spectrum has smallest difference from those of the adjacent defoci.
Figure 1711. (a) Calculated radial Fourier scans for two images taken at defocus settings of -150 and -160 nm, and (b) The Fourier ratio of the two different defoci. Adapted from 
 Peter D. Miller and J. Murray Gibson, Connecting small-angle di¤raction with real-space images by quantitative transmission electron microscopy of
amorphous thin-Þlms, Ultramicroscopy 74 (1998) 221-235.