Accurate, automatic determination of astigmatism and phase with Ctfplotter in IMOD.

Ctfplotter in the IMOD software package is a flexible program for determination of CTF parameters in tilt series images. It uses a novel approach to find astigmatism by measuring defocus in one-dimensional power spectra rotationally averaged over a series of restricted angular ranges. Comparisons with Ctffind, Gctf, and Warp show that Ctfplotter's estimated astigmatism is generally more reliable than that found by these programs that fit CTF parameters to two-dimensional power spectra, especially at higher tilt angles. In addition to that intrinsic advantage, Ctfplotter can reduce the variability in astigmatism estimates further by summing results over multiple tilt angles (typically 5), while still finding defocus for each individual image. Its fitting strategy also produces better phase estimates. The program now includes features for tuning the sampling of the power spectrum so that it is well-represented for analysis, and for determining an appropriate fitting range that can vary with tilt angle. It can thus be used automatically in a variety of situations, not just for fitting tilt series, and has been integrated into the SerialEM acquisition software for real-time determination of focus and astigmatism.