Tilt-series-based joint CTF estimation for cryo-electron tomography

Contrast transfer function (CTF) estimation is a necessary step in the cryo-electron tomography (cryoET) workflow and essential for high-resolution in situ structural determination. However, the low signal-to-noise ratio and continuous defocus variation in micrographs of cryoET tilt series make accurate CTF estimation challenging. Here, we report a tilt-series-based joint CTF estimation method implemented in the new software CTFMeasure. The joint estimation method combines all Thon-ring signals in a tilt series to improve the estimation accuracy. By using an objective function involving the CTF parameters and geometric parameters of a cryoET tilt series, CTFMeasure can estimate the CTF parameters of each micrograph and the absolute tilt angle offset of the lamellar sample relative to the sample stage plane, which is usually the glancing angle used during focused ion beam (FIB) milling. Tests on both synthetic and experimental data, as well as subtomogram averaging, demonstrated the accurate CTF estimation of cryoET tilt series by CTFMeasure.