Contrast transfer function

About: Contrast transfer function is a research topic. Over the lifetime, 934 publications have been published within this topic receiving 26533 citations.

Aberration Corrected Analytical Scanning and Transmission Electron Microscope for High-Resolution Imaging and Analysis for Multi-User Facilities

Abstract: In recent years the revolution in aberration correction technology has made ultrahigh resolution imaging and analysis routinely accessible on transmission electron microscope (TEM) and scanning transmission electron microscope (STEM). We have developed a new analytical 200 kV cold field emission TEM equipped with a probe-forming aberration corrector, the model is Hitachi HF5000 (Figure 1). The microscope is fully covered in a metal enclosure to reduce the influence from environmental acoustic noise and temperature variation. Remote operation through Ethernet communication is possible as a result of a new design individual microprocessor circuit. Regarding the atomically resolved analytical capability, one of the key demands is to achieve high performance at a multi-user facility. To meet this demand, the Hitachi HF5000 is designed to be user friendly and extensive sample capability covers most requirement s from users in the fields of material science, materials fabrication, and device industry. The HF5000 is capable of TEM imaging, STEM imaging with bright field (BF), annular dark field (DF) detectors, and secondary electron (SE) imaging. The probe-forming aberration corrector with automated correction of up to third order aberrations allows users to obtain aberration-free STEM illumination optics with minimized effort. Figure 2 gives an example after the aberration correction, the Ronchigram pattern of the amorphous specimen shows an approximately 32 mrad half angle flat region, corresponding to the optimal aperture condition for aberration-free STEM imaging. While TEM and STEM imaging probe the bulk structure of specimens, the SE imaging helps understanding the surface structure. It is important to note that the SE image can be acquired simultaneously with STEM image therefore both surface and bulk structures are revealed side-by-side at the same time, even at atomic resolution [1]. Such a triple imaging capability on one microscope column is very unique and critical in studying heterogeneous materials such as catalysts.

CTF Correction in Cryo-Electron Tomography

Abstract: Nanometer resolution inside the cell will allow us to study the fundamentals of life at the smallest scale. This thesis addresses what is needed to obtain this resolution using cryo-electron tomography (CET). CET is a microscopy modality with the unique potential to visualize proteins, protein-complexes and other molecular assemblies in a close-to-native environment at a high resolution in three dimensions. In CET, a thin specimen embedded in vitreous ice is tilted in the electron beam to acquire projections under different angles. The primary contrast mechanism is phase contrast which is obtained by intentionally defocussing the specimen. The contrast transfer function (CTF) describes how aberrations, such as defocussing, generate detectable intensity contrast. The CTF is an oscillating function of spatial frequency, resulting in contrast inversions at certain spatial frequencies. To interpret structures at a resolution beyond the first zero-crossing, it is necessary to correct for the CTF. In this thesis we answer the questions: how can we model the CTF for tomographic geometries, what is the influence of CTF correction, which processing steps need to be improved to fully exploit CTF correction in combination with subtomogram averaging, and how big is the improvement in resolution? This thesis presents fast and efficient algorithms for both forward modeling and correction of the CTF for tilted geometries of various thicknesses, as well as methods to model the specimen-beam interaction. To avoid a brute-force multislice procedure to model the specimen-beam interaction, we study the influence of the projection assumption, the weak-phase object approximation, and the thick-phase grating approximation, as well as their limits of applicability. Fast algorithms for computing and correcting the CTF in tilted geometries are mandatory for practical use. Our algorithm reduces the computation time for a tilt-series from ~100 hours down to ~45 minutes. Using simulations, we also study how different CTF models influence the projections and what the influence of CTF correction is on the final reconstruction. We quantify the influence of the developed CTF correction methods in subtomogram averaged CET. Subtomogram averaging is the solution to raise the signal-to-noise ratio for high spatial frequencies above the noise floor. To achieve the required defocus estimation accuracy under realistic experimental conditions, we present an extended acquisition scheme in combination with a previously developed defocus estimation procedure. Using simulations and experimental data of ribosomes, acquired on a Titan microscope (FEI Company) at the NeCEN, we study the influence on the achievable resolution of different processing steps, including CTF correction, as well as the number of subtomograms. A comparison of simulations and experiments allows us to identify the factors that limit the resolution as well as the effect of tilted CTF correction. We obtained a final average using 3198 ribosomes with a resolution of 2.2 nm on the experimental data. Our simulations suggest that with the same number of particles a resolution of 1.2 nm could be achieved by improving the tilt-series alignment.

Cross-sectional image obtained from spherical aberration-free three-dimensional image intensity distribution in transmission electron microscopy

Abstract: Using a three-dimensional image intensity distribution obtained by spherical aberration-corrected transmission electron microscopy, we studied a cross-sectional image (x-z image) of a gold crystal observed along the z-axis. In this x-z image, the bending of the interference fringes was observed in the edge region. We demonstrated that the bending is caused by a relative phase shift between the electron waves induced by dynamical electron scattering. By comparing with simulated images, the relative phase shift of about π/4 was proved to correspond to a difference in thickness of ∼0.9 nm.

A Model for Human Tooth Enamel Central Dark Line its Hrtem Images Contrast Transfer Function Analysis

Abstract: When the enamel crystallites are observed with the transmission electron microscope (TEM), they exhibit a line of 1 to 1.5 nm wide along their centers [1,2]. This line has been named “dark line”, although in reality its contrast is focus dependent: it appears dark in underfocus, disappears when the image goes through focus, and is white in overfocus. Experimental evidences suggested the presence of Octocalcium Phosphate(OCP) and Hydroxyapatite(HA) in Central Dark Line(CDL).

Refractive index retrieval by combining the contrast transfer function and SART in X-ray in-line phase tomography

Abstract: This work presents a new iterative algorithm for synchrotron radiation micro-tomography, using multidistance propagation-based phase contrast imaging. Up to now, phase retrieval and tomographic reconstruction were processed as two separated problems. Here, we combine these two parts into a single step algorithm (CTF-SART). A linearized version of the contrast model (known as the contrast transfer function, CTF) was used for phase retrieval, and the simultaneous algebraic reconstruction technique (SART) for the tomographic reconstruction. We present the theoretical framework of the method and the first tests on simulated data.