Showing papers on "Contrast transfer function published in 2017"
TL;DR: An in-focus data acquisition method for cryo-EM single-particle analysis with the Volta phase plate is extended to include a small amount of defocus which enables contrast transfer function measurement and correction, which simplifies the experiment and increases the data acquisition speed.
Abstract: Previously, we reported an in-focus data acquisition method for cryo-EM single-particle analysis with the Volta phase plate (Danev and Baumeister, 2016). Here, we extend the technique to include a small amount of defocus which enables contrast transfer function measurement and correction. This hybrid approach simplifies the experiment and increases the data acquisition speed. It also removes the resolution limit inherent to the in-focus method thus allowing 3D reconstructions with resolutions better than 3 A.
107 citations
TL;DR: In this article, the integrated differential phase contrast (iDPC-STEM) technique was proposed to combine light and heavy elements together in low-frequency transfer with an ideal first moment detector.
Abstract: Scanning transmission electron microscopy (STEM) imaging, which has been in use for many decades, is analyzed mathematically for thin nonmagnetic samples. The result is a closed-form description of a general STEM image, showing that STEM imaging is, in general, nonlinear (contrast transfer is sample dependent), except when an ideal first moment detector is used. The closed-form description is subsequently used to optimize STEM imaging. We distinguish between STEM techniques using symmetric scalar detectors and antisymmetric vector detectors and show that for both cases practical experimental techniques can be defined that are approximately linear. The case of antisymmetric vector detectors yields the newly introduced integrated differential phase contrast (iDPC-STEM) technique. For this technique we show experimental results, showing that it is capable of imaging light and heavy elements together as well as giving full low-frequency transfer. We demonstrate that it can be used under low-dose conditions.
48 citations
TL;DR: This paper applies the concept of phase modulation to the correction of spherical aberration in a scanning transmission electron microscope and demonstrates an improvement in spatial resolution.
Abstract: Recent progress in phase modulation using nanofabricated electron holograms has demonstrated how the phase of an electron beam can be controlled In this paper, we apply this concept to the correction of spherical aberration in a scanning transmission electron microscope and demonstrate an improvement in spatial resolution Such a holographic approach to spherical aberration correction is advantageous for its simplicity and cost-effectiveness
19 citations
TL;DR: A proof-of-principle experiment is shown that demonstrates successful correction of the spherical aberration in STEM by means of such a grating corrector (GCOR), which enables us to record aberration-corrected high-resolution high-angle annular dark field STEM images, although yet without advancement in probe current and resolution.
18 citations
TL;DR: The application of combined chromatic and spherical aberration correction in high-resolution transmission electron microscopy enables a significant improvement of the spatial resolution down to 50 pm and it is demonstrated that such a resolution can be achieved in practice at 200kV.
15 citations
TL;DR: This paper analyzes the influence of spherical aberration on the depth of focus of symmetrical optical systems for imaging of axial points using ray equations in the image plane and considering longitudinal spherical Aberration as well.
Abstract: This paper analyzes the influence of spherical aberration on the depth of focus of symmetrical optical systems for imaging of axial points. A calculation of a beam's caustics is discussed using ray equations in the image plane and considering longitudinal spherical aberration as well. Concurrently, the influence of aberration coefficients on extremes of such a curve is presented. Afterwards, conditions for aberration coefficients are derived if the Strehl definition should be the same in two symmetrically placed planes with respect to the paraxial image plane. Such conditions for optical systems with large aberrations are derived with the use of geometric-optical approximation where the gyration diameter of the beam in given planes of the optical system is evaluated. Therefore, one can calculate aberration coefficients in such a way that the optical system generates a beam of rays that has the gyration radius in a given interval smaller than the defined limit value. Moreover, one can calculate the maximal depth of focus of the optical system respecting the aforementioned conditions.
11 citations
TL;DR: This work analytically derive the relation between sample shift and defocus, and applies the results to the measurement and analysis of achromats in an aberration-corrected LEEM instrument.
9 citations
TL;DR: It is found that lens aberrations, and spatial and temporal coherence may affect the validity of the CTF approach to model LEEM image formation under certain conditions, and the foundation for quantitative image evaluation using these methods is laid.
6 citations
TL;DR: The geometric and chromatic aberration coefficients of the probe-forming system in an aberration corrected transmission electron microscope have been measured using a Ronchigram recorded from monolayer graphene using an auto-correlation function.
6 citations
TL;DR: The purpose of this paper is to characterize the spherical aberration of a microscope objective lens by using diffraction light from nanosphere particles to measure optical aberrations with a good accuracy.
Abstract: The purpose of this paper is to characterize the spherical aberration of a microscope objective lens by using diffraction light from nanosphere particles The experimental image of the diffraction spot of a nanosphere is fitted with the Nijboer-Zernike model to estimate the spherical aberration The method can easily be extended to the measurement of other and higher-order aberrations Noticeable features of this new measurement technique are real-time measurements, simple structure, and flexibility, which lead it to measure optical aberrations with a good accuracy
TL;DR: In this article, a novel adaptive lens with two degrees of freedom was proposed for axial scanning and aberration correction in confocal microscopy, which enabled both axial scan and correction of spherical aberrations.
Abstract: Deformable mirrors are the standard adaptive optical elements for aberration correction in confocal microscopy. Their usage leads to increased contrast and resolution. However, these improvements are achieved at the cost of bulky optical setups. Since spherical aberrations are the dominating aberrations in confocal microscopy, it is not required to employ all degrees of freedom commonly offered by deformable mirrors. In this contribution, we present an alternative approach for aberration correction in confocal microscopy based on a novel adaptive lens with two degrees of freedom. These lenses enable both axial scanning and aberration correction, keeping the setup simple and compact. Using digital holography, we characterize the tuning range of the focal length and the spherical aberration correction ability of the adaptive lens. The operation at fixed trajectories in terms of focal length and spherical aberrations is demonstrated and investigated in terms of reproducibility. First results indicate that such adaptive lenses are a promising approach towards high-resolution, high-speed three-dimensional microscopy.
TL;DR: In this paper, a 3D polarization ray-tracing matrix was combined with the optical path difference to obtain a three-dimensional polarization aberration function, which avoided the need for a complicated phase unwrapping process.
29 Mar 2017
TL;DR: Adaptive Optics as discussed by the authors is a technique that was originally developed in optical astronomy to solve the problem of optical aberrations in microscopy, which produces a distorted wavefront at the focus of the imaging system leading to a non-optimum focal spot, resulting in a decrease in image resolution and a deterioration in image quality.
Abstract: All forms of optical microscopy have the potential to suffer from aberrations due to misalignments in the optical system, local refractive index changes in the sample, or, in many cases, both. Aberrations produce a distorted wavefront at the focus of the imaging system leading to a non-optimum focal spot, resulting in a decrease in image resolution and hence a deterioration in image quality. The problem is particularly prevalent when imaging biological tissue using an optical sectioning microscope where the improved axial resolution over standard wide-field techniques leads the user to image deeper into their sample than ever before. The structure present in the tissue presents complex axial and lateral variations in refractive indices, inhomogeneities that increase as the thickness of tissue the light passes through increases. Adaptive optics, a technique that originated in optical astronomy, poses a powerful solution to the problem. The principle behind adaptive optics involves shaping the wavefront of the incoming light in such a way so as to overcome the distortions imposed by the sample and imaging system. Crucial to the successful implementation of adaptive optics in microscopy is the method used to determine the wavefront correction required. Here we introduce the concepts behind adaptive optics, discuss several approaches that have been taken to implement adaptive optics into microscopy, and finally provide examples of its success when applied to a variety of imaging modalities such as multiphoton microscopy, stimulated emission depletion microscopy, and selective plane illumination microscopy.
01 May 2017
TL;DR: In this article, the authors demonstrate that the use of extended sources can improve low frequency performance and propose to use source shape as a parameter that can be used when optimizing combinations of measurements to produce robust phase reconstructions.
Abstract: Propagation-based phase retrieval using the contrast transfer function (CTF) allows images at any propagation distance to be used when recovering the phase of slowly-varying objects. The CTF suffers from artifacts due to nulls in the transfer function at low spatial frequency and at higher, propagation-distance-dependent frequencies, though the latter can be alleviated by combining measurements at multiple distances. We demonstrate that the use of extended sources can improve low frequency performance. In addition, this method offers source shape as a parameter that can be used when optimizing combinations of measurements to produce robust phase reconstructions.
TL;DR: In this paper, the effect of spherical aberration on imaging performance of wavefront coding systems with a cubic phase mask is presented by ray aberration and spot diagram, and the results show that the wave front coding systems have a high tolerance to spherical aberrations through a given defocus range.
14 May 2017
TL;DR: In this paper, the authors investigated the focusing property of an annular-shaped beam in the presence of strong spherical aberration and found that it is robust against optical aberration.
Abstract: We experimentally investigated the focusing property of an annular-shaped beam. Apparent robustness against optical aberration was revealed when an annular-shaped beam is tightly focused in the presence of strong spherical aberration.
26 Jun 2017
TL;DR: In this article, the influence of spherical aberration coefficients on the depth of focus of optical systems is analyzed and the conditions for aberration coefficient are derived for two cases when either the Strehl definition or the gyration radius should be identical in two symmetric planes with respect to the paraxial image plane.
Abstract: This contribution describes how to model the influence of spherical aberration coefficients on the depth of focus of
optical systems. Analytical formulas for the calculation of beam's caustics are presented. The conditions for aberration
coefficients are derived for two cases when we require that either the Strehl definition or the gyration radius should be
the identical in two symmetrically placed planes with respect to the paraxial image plane. One can calculate the
maximum depth of focus and the minimum diameter of the circle of confusion of the optical system corresponding to
chosen conditions. This contribution helps to understand how spherical aberration may affect the depth of focus and how
to design such an optical system with the required depth of focus. One can perform computer modelling and design of
the optical system and its spherical aberration in order to achieve the required depth of focus.
TL;DR: Combining the impact position on the detector and the time of flight of electrons, the spherical aberration can be corrected and the energy resolution can be significantly improved, 1.5× in the case of the double toroidal analyser.
Abstract: In an energy-dispersive electron spectrometer, the electrons with the same kinetic energy but different polar angles fly along different paths and impinge upon the detector at different locations. This behavior materializes the spherical aberration of the electron optics, which deteriorates the focussing quality on the detector, and thus the energy resolution of the instrument. Here, we demonstrate that, in general, the electron time of flight changes monotonically as a function of the polar angle. Combining the impact position on the detector and the time of flight of electrons, the spherical aberration can be corrected and the energy resolution can be significantly improved, 1.5× in the case of our double toroidal analyser. This correction method has a general applicability and can be of interest to experimentalists willing to push further the performances of their electron spectrometers when the time of flight is available.
TL;DR: In the current work, reporting holo-TIE imaging of mouse macrophage cells, OsO4 was found to create a uniform background that identifies only the approximate shape of the cytoplasm-filled regions, while BaSO4 particles were found to stand out nicely.
Abstract: In this issue of Acta Crystallographica Section A, a significant advance in full-field X-ray imaging of biological samples is reported by workers from Tim Salditt’s group at GeorgAugust-University in Göttingen (Krenkel et al., 2017). Their holographic regime method, which they call the holo-TIE approach, is a significant improvement of the classical ‘transport of intensity’ (TIE) method of Paganin & Nugent (1998). Following the original development of Cloetens et al. (1999), the work described by Krenkel et al. combines data measured at multiple detector distances to fill gaps of missing frequencies in the contrast-transfer function. This idea is presented and justified using the language of variation of Fresnel numbers. The results also clearly show the respective advantages of different staining strategies relevant to biological imaging, where both resolution and contrast are key metrics. In X-ray imaging science, ‘resolution’ is defined as the highest spatial frequency capable of being measured by the instrument, limited by the solid angle passed by some aperture or by the detector, for example. The ‘contrast’, on the other hand, is a property of the sample, measured in an analogous way to the presence of density (or phase) modulations of a given spatial frequency within the sample. Both the instrument and the sample have to deliver this level of performance in order for the resulting image to contain the fine features needed for biological interpretation. In the current work, reporting holo-TIE imaging of mouse macrophage cells (Krenkel et al., 2017), OsO4 was found to create a uniform background that identifies only the approximate shape of the cytoplasm-filled regions, while BaSO4 particles were found to stand out nicely. However, while the BaSO4 particles are seen with high resolution, they are markers that may or may not report on the biological state of the sample, depending on the method of attachment and introduction to the cells. Observing the markers with high resolution does not necessarily mean that the biological functions are determined with the same level of detail.
TL;DR: In this paper, Ernst Ruska-Center for Microscopy and Spectroscopy with Electrons, Jülich-Aachen Research Alliance (JARA), Forschungszentrum Jürlich GmbH, 52425 Julewitz, Germany.
Abstract: 1. Ernst Ruska-Center for Microscopy and Spectroscopy with Electrons, Jülich-Aachen Research Alliance (JARA), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany. 2. Central Facility for Electron Microscopy, RWTH Aachen University, 52074 Aachen, Germany. 3. School of Electronic and Information Engineering and State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710049, China.
TL;DR: In this article, the authors demonstrate strategies for correcting temporal incoherence, allowing true quantitative comparison of experiment and simulation, and demonstrate how to align a series of fast scanned images to obtain a useful image.
Abstract: Quantitative analysis of high voltage scanning transmission electron microscope (STEM) images using annular dark field (ADF) has become routine [1]. Advances in aberration correction has extended atomic resolution imaging to lower incident electron energies suitable for the imaging of 2D materials such as BN and graphene [2,3]. Lower energies, such as 60 keV, reduce knock-on damage but in turn greatly increase the effects of temporal incoherence, leading to extended probe tails and reduced contrast. In addition, the signal to noise ratio of images of 2D materials is also quite low, since the electron beam is scattered by only a few atoms, rather than an extended atomic column. Even with lower energies, some specimens are still prone to beam damage and a series of fast scanned images is often averaged to obtain a useful image. This raises the issue of image alignment or registration. In this work we demonstrate strategies for correcting temporal incoherence, allowing true quantitative comparison of experiment and simulation.
01 Jan 2017
TL;DR: In this article, the authors derived the formula of the phase shift of a convex lens and showed that it is a kind of phase shifter depending on the incident angle of the optical ray to the lens.
Abstract: As explained in Chap. 16, a lens is a kind of phase shifter depending on incident angle of optical ray to the lens. In this section, we derive the formula of the phase shift. Let us start with the function of a convex lens.