CTF determination and correction for low dose tomographic tilt series.

The resolution of cryo-electron tomography can be limited by the first zero of the microscope's contrast transfer function (CTF). To achieve higher resolution, it is critical to determine the CTF and correct its phase inversions. However, the extremely low signal-to-noise ratio (SNR) and the defocus gradient in the projections of tilted specimens make this process challenging. Two programs, CTFPLOTTER and CTFPHASEFLIP, have been developed to address these issues. CTFPLOTTER obtains a 1D power spectrum by periodogram averaging and rotational averaging and it estimates the noise background with a novel approach, which uses images taken with no specimen. The background-subtracted 1D power spectra from image regions at different defocus values are then shifted to align their first zeros and averaged together. This averaging improves the SNR sufficiently that it becomes possible to determine the defocus for subsets of the tilt series rather than just the entire series. CTFPHASEFLIP corrects images line-by-line by inverting phases appropriately in thin strips of the image at nearly constant defocus. CTF correction by these methods is shown to improve the resolution of aligned, averaged particles extracted from tomograms. However, some restoration of Fourier amplitudes at high frequencies is important for seeing the benefits from CTF correction.

Physical characterization of a high-resolution CCD detector for mammography.

The physical characteristics of charge-coupled device (CCD) mammography detector with 16-bit dynamic range and 27 microm detector element size were investigated. The detector, with an active area of 1 cm x 20 cm is suitable for slot-scanning systems. We evaluated the detector resolution by measuring the modulation transfer function (MTF) using a tilted edge. We also measured the noise power spectra (NPS) and detective quantum efficiency (DQE) using tungsten spectra filtered with 3 mm Al. We carried out measurements in two modes of operation: the frame mode where the detector is stationary and the scan mode where the detector operates in a slot-scanning configuration. The specific beam qualities and exposure ranges employed were 30 kVp, HVL 1.4 mm Al, 1.24 microC kg(-1) to 12.44 microC kg(-1), and 40 kVp, HVL 2.1 mm Al and 3.26 microC kg(-1) to 16.64 microC kg(-1). The product of the normalized noise power spectrum and exposure was also computed to evaluate the quantum limited characteristic of the detector. The detector MTF was 12% at 15 lp mm(-1). The product of the noise power spectra and exposure was independent of exposure level, indicating a quantum limited detector. The DQE in the scan and frame modes near zero frequency was 40% and 60%, respectively. Our results show that the slot-scanning configuration was less efficient than the performance capabilities of the detector. This detector is comparable to other digital mammography sensors evaluated in the literature.