Contrast Transfer Research Articles

Use of testate amoebae to infer paleohydrology during fen and fen-bog transition stages of ombrotrophic mire development

We evaluated the feasibility of using testate amoebae to infer the quantitative paleohydrology of ombrotrophic mires during their early stages (fen and fen-bog transition) of development. Two transfer functions, one derived from ombrotrophic and the other from minerotrophic mires, were applied to a peat core from an ombrotrophic mire in a taiga region of west Siberia. An ombrotrophic transfer function was applied to the bog stage of mire development. In contrast, ombrotrophic and minerotrophic transfer functions were applied independently to infer water table depth in the fen and fen-bog transition stages. Results of the two approaches for calculating water table depth during the fen and fen-bog transition stages differed by as much as 38 cm for the same peat sample. The main reason for this discrepancy is presence of testate amoeba taxa (e.g. Centropyxis aculeata, Cyclopyxis eurystoma, Cyclopyxis eurystoma v. parvula) in the peat that inhabit both modern ombrotrophic and minerotrophic mires, but differ substantially, in cases by > 20 cm, in terms of their water table depth optima in the ombrotrophic and minerotrophic mire calibration data sets. This difference in inferred water table depth also stems, to a lesser degree, from the fact that the ombrotrophic mire model does not include taxa that inhabited exclusively minerotrophic mires in the fen and fen-bog transition stages. Given these findings, we propose that different models be used for different stages of development, to reconstruct past water table depth in ombrotrophic mires. We recommend use of a model based solely on the ombrotrophic mire data set for the bog stage, and application of a second model based on the minerotrophic mire data set, for the fen and fen-bog transition stages. Application of an ombrotrophic model to the early stages of bog development can yield erroneous paleohydrological reconstructions.

The Light Sword Lens and its usefulness for presbyopia reduction

AbstractPurposeTo evaluate the light sword lens ‐ an optical imaging element with extended depth of focus and angularly varying optical power for compensation of presbyopia.MethodsTwo novel light sword lenses were compared with commercially available intraocular lenses with the help of an optical system for intraocular lens testing certified according to the requirements of the International Organization for Standardization. The point spread function, the modulation transfer function for 50 lines/mm and the modulation transfer function area (MTFa) ratio were measured.ResultsThe light sword lenses exhibit a point spread function with a distinct maximum in the whole designed defocus range (0‐3D or 0‐4D). Contrast transfer ratio maintains higher values than 0.2 for defocus at least up to 2.5 D.ConclusionsUnlike the hitherto known solutions, the light sword lens permits to obtain high uniformity of the contrast transfer function and focusing within a range of defocus extending to the value of 3D. Therefore the proposed concept seems to be very promising for a development of presbyopia‐correcting intraocular lenses capable to restore a high quality functional vision substituting lost accommodation range.

Robust contrast-transfer-function phase retrieval via flexible deep learning networks.

By exploiting the total variation (TV) regularization scheme and the contrast transfer function (CTF), a phase map can be retrieved from single-distance coherent diffraction images via the sparsity of the investigated object. However, the CTF-TV phase retrieval algorithm often struggles in the presence of strong noise, since it is based on the traditional compressive sensing optimization problem. Here, convolutional neural networks, a powerful tool from machine learning, are used to regularize the CTF-based phase retrieval problems and improve the recovery performance. This proposed method, the CTF-Deep phase retrieval algorithm, was tested both via simulations and experiments. The results show that it is robust to noise and fast enough for high-resolution applications, such as in optical, x-ray, or terahertz imaging.

3037 Spontaneous Cystgastrostomy From Pancreatic Pseudocyst Erosion Into Gastric Wall Resulting in Gastrointestinal Hemorrhage

INTRODUCTION: Pancreatic pseudocysts are a common complication of pancreatitis. Spontaneous erosion of a pseudocyst into adjacent organs is rare, manifesting in a variety of clinical symptoms and presentations. We present a case of spontaneous fistulization of a pancreatic pseudocyst into the stomach resulting in life-threatening bleeding. CASE DESCRIPTION/METHODS: A 60-year-old gentleman with history of type 2 diabetes mellitus, hypertension and chronic pancreatitis with known pancreatic pseudocyst presented with multiple episodes of melena associated with fatigue, weakness and epigastric pain aggravated by food intake. He denied history of peptic ulcer disease but admitted to chronic NSAID use. Physical examination revealed a pale patient with mild generalized abdominal tenderness without signs of peritonitis. Melenic stools were noted on digital rectal exam. Labs were significant for critical normocytic anemia with Hgb 6.3 g/dL. CT scan of abdomen and pelvis showed an 11.7 × 9 cm lesion in the pancreatic body with calcified rim communicating with gastric antrum. Gastrograffin swallow showed contrast transfer from stomach into the pseudocyst. A CT-Angiogram of the abdomen and pelvis failed to reveal a source of bleeding or peripancreatic pseudoaneurysms. Patient underwent EGD which showed 1 centimeter antral fistula-opening representing a spontaneous cystogastric fistula. No ulcers were found. The patient eventually underwent surgical excision of pancreatic pseudocyst, antrectomy and Billroth-II reconstruction. DISCUSSION: Pseudocysts complicate 20-40% of chronic pancreatitis. They can cause pain, bowel obstruction, infection, or hemorrhage. Treatment is indicated when cysts become symptomatic or grow beyond 5 cm. However, pseudocysts often resolve by spontaneous drainage into the pancreatic ductal system. Rarely, they can rupture into the peritoneal cavity or erode into nearby hollow organs. Bleeding can be the result of pseudocyst erosion into nearby vessels or rupture of nearby pseudoaneurysms. While involvement of gastroduodenal, splenic, hepatic and inferior pancreaticoduodenal arteries has been reported, none of these sources could be identified in this case. Treatment can take the form of direct embolization or surgical hemostasis. In summary, we have presented a case of pancreatic pseudocyst with spontaneous cystogastric fistula formation accompanied by massive upper GI bleeding eventually treated by surgical excision and Billroth-II reconstruction.

High-speed x-ray imaging system for the investigation of laser welding processes

A high-speed x-ray imaging system was built to investigate the fundamentals of laser material processing, such as laser welding. The system allows visualizing and analyzing the laser-induced process dynamics occurring also inside optically nontransparent workpieces. The details of the setup are presented together with the resulting performance with regard to edge sharpness, contrast, contrast transfer, and spatial as well as temporal noise. For voids with a depth (in respect to the x-ray radiation) of 100–500 μm, which is a typical range for focal diameters used in laser beam welding, a maximum contrast of 3%–19%, respectively, can be achieved. Due to the edge blurring, caused by the imaging system, the contrast is further decreased by 20% for voids with a lateral size of 100 μm and less than 10% for voids with a lateral size of 500 μm, when a magnification of 5.4 is used. The image intensifier, needed to increase the number of photons to saturate the camera, induces a noise floor of ±15% in respect to the mean gray value and results in a maximum achievable signal to noise ratio for a 100 μm step of 1.2.

Transmission point spread function of a turbid slab.

A transmission point spread function characterizes the spatial distribution of light transmitted through a turbid slab. Because of scatter due to turbidity, light diffuses and the distribution of photons on exiting the slab may be very different from that upon entering the slab. Using the multiple-path model of reflection and transmission, the transmission point spread function and related modulation transfer function are derived. The analytic expression for the point spread function is compared to a Monte Carlo simulation of photon transmission. The transmission modulation transfer function is used to define a measure of visibility through the turbid slab-a contrast transfer function.

Design for a 10 keV multi-pass transmission electron microscope

Multi-pass transmission electron microscopy (MPTEM) has been proposed as a way to reduce damage to radiation-sensitive materials. For the field of cryo-electron microscopy (cryo-EM), this would significantly reduce the number of projections needed to create a 3D model and would allow the imaging of lower-contrast, more heterogeneous samples. We have designed a 10 keV proof-of-concept MPTEM. The column features fast-switching gated electron mirrors which cause each electron to interrogate the sample multiple times. A linear approximation for the multi-pass contrast transfer function (CTF) is developed to explain how the resolution depends on the number of passes through the sample.

Analysis of depth-sectioning STEM for thick samples and 3D imaging

We derive a model that describes 3D volume imaging in depth-sectioning STEM that is valid for all STEM techniques under three well-defined conditions: linearity, undisturbed probe and elastic scattering. The resulting undisturbed probe model generalizes the widely used idea that the undisturbed probe intensity in three dimensions can be used as the point spread function for depth-sectioning ADF-STEM to all STEM techniques including (A)BF- and iDPC-STEM. The model provides closed expressions for depth-sectioning STEM, which follow directly from the 2D expressions for thin samples, and thereby enables analysis of the 3D resolution. Using the model we explore the consequences of the resulting 3D contrast transfer function (CTF) for the z-resolution at different length scales and illustrate this with experiments. We investigate the validity and limitations of the model using multi-slice simulations showing that it is valid and quantitatively accurate for relatively thick amorphous samples but not for crystalline samples in zone-axis due to channeling. We compare depth-sectioning in iDPC- and ADF-STEM and show that iDPC-STEM can extract information from deeper into the sample, all the way till the bottom of the sample, thereby effectively allowing a thickness measurement. Also the difference in optimal focus conditions between iDPC- and ADF-STEM is explained. Finally, we propose practical criteria for deciding whether a sample is thin or thick.

Contrast Transfer and Noise Minimization in Electron Ptychography

Journal Article Contrast Transfer and Noise Minimization in Electron Ptychography Get access Colum M O'Leary, Colum M O'Leary University of Oxford, Department of Materials, Oxford, UK Search for other works by this author on: Oxford Academic Google Scholar Gerardo T Martinez, Gerardo T Martinez University of Oxford, Department of Materials, Oxford, UK Search for other works by this author on: Oxford Academic Google Scholar Emanuela Liberti, Emanuela Liberti University of Oxford, Department of Materials, Oxford, UKelectron Physical Sciences Imaging Centre (ePSIC), Diamond Light Source, UK Search for other works by this author on: Oxford Academic Google Scholar Martin J Humphry, Martin J Humphry Phasefocus Ltd, Sheffield, UK Search for other works by this author on: Oxford Academic Google Scholar Angus I Kirkland, Angus I Kirkland University of Oxford, Department of Materials, Oxford, UKelectron Physical Sciences Imaging Centre (ePSIC), Diamond Light Source, UK Search for other works by this author on: Oxford Academic Google Scholar Peter D Nellist Peter D Nellist University of Oxford, Department of Materials, Oxford, UK Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 25, Issue S2, 1 August 2019, Pages 64–65, https://doi.org/10.1017/S1431927619001053 Published: 01 August 2019

Contrast transfer function of de-noising algorithms.

This paper presents a comprehensive study on the contrast transfer function of de-noising algorithms. In order to cover a broad variety of methods, 45 de-noising algorithms are chosen considering their recognized efficiency in the different application domains of image processing. Advanced methods are targeted: wavelet transform-based algorithms with Daubechies, symlets, curvelets, contourlets, patch-based methods such as BM3D, NL-means algorithms and deep learning approaches; in addition, classical spatial filtering methods are considered, such as Wiener, median, Gauss filtering, and adaptive filtering approaches such as anisotropic diffusion and synthetic aperture radar filtering. The contrast transfer function is provided for each algorithm. Ranking of the set of de-noising algorithms is established according to proposed metrics. The paper provides practical methodology and novel results dedicated to the evaluation of the contrast transfer function of de-noising approaches from literature.

Optimal illumination scheme for isotropic quantitative differential phase contrast microscopy

Differential phase contrast microscopy (DPC) provides high-resolution quantitative phase distribution of thin transparent samples under multi-axis asymmetric illuminations. Typically, illumination in DPC microscopic systems is designed with two-axis half-circle amplitude patterns, which, however, result in a non-isotropic phase contrast transfer function (PTF). Efforts have been made to achieve isotropic DPC by replacing the conventional half-circle illumination aperture with radially asymmetric patterns with three-axis illumination or gradient amplitude patterns with two-axis illumination. Nevertheless, the underlying theoretical mechanism of isotropic PTF has not been explored, and thus, the optimal illumination scheme cannot be determined. Furthermore, the frequency responses of the PTFs under these engineered illuminations have not been fully optimized, leading to suboptimal phase contrast and signal-to-noise ratio for phase reconstruction. In this paper, we provide a rigorous theoretical analysis about the necessary and sufficient conditions for DPC to achieve isotropic PTF. In addition, we derive the optimal illumination scheme to maximize the frequency response for both low and high frequencies (from 0 to 2NAobj) and meanwhile achieve perfectly isotropic PTF with only two-axis intensity measurements. We present the derivation, implementation, simulation, and experimental results demonstrating the superiority of our method over existing illumination schemes in both the phase reconstruction accuracy and noise-robustness.

High contrast STEM imaging for light elements by an annular segmented detector

Annular bright-field scanning transmission electron microscopy (ABF STEM) has been actively used to directly observe the light element atoms inside materials and devices. However, the detector angle condition for conventional ABF STEM has been empirically selected and thus is not always optimized for observing ultra-light element atoms such as hydrogen and lithium atoms. In this study, the detector conditions for ABF STEM were reexamined by calculating a new type of phase contrast transfer function (PCTF) for an annularly segmented detector to maximize the image contrast of ultra-light element atoms such as lithium. Using this new PCTF, an improved detector geometry for observing lithium atoms is demonstrated, which is confirmed by the image simulations and experiments in several types of lithium cathode materials.

Fourier optics of image formation in aberration-corrected LEEM

We present the extended Fourier Optics (FO) approach for modeling image formation in aberration-corrected low energy electron microscopy (ac-LEEM). The FO formalism is also generalized for image simulations of one or two-dimensional objects in ac and uncorrected (nac) LEEM. A comparison is made of the extended FO approach presented here and the extended contrast transfer function (CTF) approach for ac-LEEM that was developed earlier. The mathematically rigorous extended FO approach gains an advantage under conditions, particularly defocus, that partial coherence of the illumination may compromise the validity of the approximate CTF intensity calculation. The drawback of the FO approach compared to the CTF approach, which is its slow computational speed, is mitigated partly here by the implementation of a multi-core, multi-threading programming architecture. This work broadens our capabilities to understand the origins of LEEM image contrast and to perform quantitative evaluation of contrast observed in an image focal series.

Frozen-hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure.

Cryo-electron tomography and small-angle X-ray scattering were used to investigate the chromatin folding in metaphase chromosomes. The tomographic 3D reconstructions show that frozen-hydrated chromatin emanated from chromosomes is planar and forms multilayered plates. The layer thickness was measured accounting for the contrast transfer function fringes at the plate edges, yielding a width of ~7.5nm, which is compatible with the dimensions of a monolayer of nucleosomes slightly tilted with respect to the layer surface. Individual nucleosomes are visible decorating distorted plates, but typical plates are very dense and nucleosomes are not identifiable as individual units, indicating that they are tightly packed. Two layers in contact are ~13nm thick, which is thinner than the sum of two independent layers, suggesting that nucleosomes in the layers interdigitate. X-ray scattering of whole chromosomes shows a main scattering peak at ~6nm, which can be correlated with the distance between layers and between interdigitating nucleosomes interacting through their faces. These observations support a model where compact chromosomes are composed of many chromatin layers stacked along the chromosome axis.

Prospective scintillation electron detectors for S(T)EM based on garnet film scintillators.

The performance of a scintillation electron detector for a scanning electron microscope and/or a scanning transmission electron microscope (S(T)EM) based on new epitaxial garnet film scintillators was explored. The LuGAGG:Ce and LuGAGG:Ce,Mg film scintillators with chemical formula (Ce0.01 Lu0.27 Gd0.74 )3-w Mgw (Ga2.48 Al2.46 )O12 were prepared and their cathodoluminescence (CL) and optical properties were studied and compared with the properties of current standard bulk single crystal YAG:Ce and YAP:Ce scintillators. More specifically, CL decay characteristics, CL emission spectra, CL intensities, optical absorption coefficients, and the refractive indices of the mentioned scintillators were measured. Furthermore, electron interaction volumes with absorbed energy distributions, photomultiplier (PMT) photocathode matchings, modulation transfer functions (MTF), and the photon transport efficiencies of scintillation detectors with the mentioned scintillators were calculated. A CL decay time for the LuGAGG:Ce,Mg film scintillator as low as 28 ns with an afterglow of only 0.02% at 1 μs after the e-beam excitation was observed. As determined from calculated MTFs, the scintillation detectors with the new film scintillators lose contrast transfer ability above 0.6 lp/pixel, while the currently commonly used YAG:Ce single crystal scintillators already do so above 0.1 lp/pixel. It was also calculated that the new studied film scintillators have an 8% higher photon transfer efficiency, even for a simple disk shape compared with the standard bulk single crystal YAG:Ce scintillator. The studied LuGAGG:Ce,Mg epitaxial garnet film scintillators were evaluated as prospective fast scintillators for electron detectors, not only in S(T)EM but also in other e-beam devices.

Enhanced electrochromic characteristics induced by Au/PEDOT/Pt microtubes in WO3 based electrochromic devices

A study has been carried out on improving electrochromic performances of tungsten trioxide (WO3) thin films-based electrochromic devices (ECDs) with inclusion of gold/poly (3, 4-ethylenedioxythiophene)/platinum (Au/PEDOT/Pt) microtubes. The deposited film characteristics were evaluated using scanning electron microscopy-energy-dispersive X-ray spectroscopy (SEM-EDS). SEM results indicated that homogeneous spreading of Au/PEDOT/Pt microtubes are successfully obtained onto the WO3 layer. The electrochromic performances such as electrochromic contrast, response times and charge transfer resistance were investigated and compared with Au/PEDOT/Pt microtubes-free system in detail. Higher optical contrast (26%) and faster response times (bleaching time (tb): 13.83 s, coloration time (tc): 19.25 s) were obtained for electrochromic device made from Au/PEDOT/Pt microtubes against an applied potential of ±2 V. Especially, Au/PEDOT/Pt microtubes-based ECD exhibited stronger electrochromic color change from transparent to blue.

Detectability of radiation-induced changes in magnetic resonance biomarkers following stereotactic radiosurgery: A pilot study

Our objective was to investigate direct voxel-wise relationship between dose and early MR biomarker changes both within and in the high-dose region surrounding brain metastases following stereotactic radiosurgery (SRS). Specifically, we examined the apparent diffusion coefficient (ADC) from diffusion-weighted imaging and the contrast transfer coefficient (Ktrans) and volume of extracellular extravascular space (ve) derived from dynamic contrast-enhanced (DCE) MRI data. We investigated 29 brain metastases in 18 patients using 3 T MRI to collect imaging data at day 0, day 3 and day 20 following SRS. The ADC maps were generated by the scanner and Ktrans and ve maps were generated using in-house software for dynamic tracer-kinetic analysis. To enable spatially-correlated voxel-wise analysis, we developed a registration pipeline to register all ADC, Ktrans and ve maps to the planning MRI scan. To interrogate longitudinal changes, we computed absolute ΔADC, ΔKtrans and Δve for day 3 and 20 post-SRS relative to day 0. We performed a Kruskall-Wallice test on each biomarker between time points and investigated dose correlations within the gross tumour volume (GTV) and surrounding high dose region > 12 Gy via Spearman’s rho. Only ve exhibited significant differences between day 0 and 20 (p < 0.005) and day 3 and 20 (p < 0.05) within the GTV following SRS. Strongest dose correlations were observed for ADC within the GTV (rho = 0.17 to 0.20) and weak correlations were observed for ADC and Ktrans in the surrounding > 12 Gy region. Both ΔKtrans and Δve showed a trend with dose at day 20 within the GTV and > 12 Gy region (rho = -0.04 to -0.16). Weak dose-related decreases in Ktrans and ve within the GTV and high dose region at day 20 most likely reflect underlying vascular responses to radiation. Our study also provides a voxel-wise analysis schema for future MR biomarker studies with the goal of elucidating surrogates for radionecrosis.

GoCTF: Geometrically optimized CTF determination for single-particle cryo-EM

Preferred particle orientation represents a recurring problem in single-particle cryogenic electron microcopy (cryo-EM). A specimen-independent approach through tilting has been attempted to increase particle orientation coverage, thus minimizing anisotropic three-dimensional (3D) reconstruction. However, focus gradient is a critical issue hindering tilt applications from being a general practice in single-particle cryo-EM. The present study describes a newly developed geometrically optimized approach, goCTF, to reliably determine the global focus gradient. A novel strategy of determining contrast transfer function (CTF) parameters from a sector of the signal preserved power spectrum is applied to increase reliability. Subsequently, per-particle based local focus refinement is conducted in an iterative manner to further improve the defocus accuracy. Novel diagnosis methods using a standard deviation defocus plot and goodness of fit heatmap have also been proposed to evaluate CTF fitting quality prior to 3D refinement. In a benchmark study, goCTF processed a published single-particle cryo-EM dataset for influenza hemagglutinin trimer collected at a 40-degree specimen tilt. The resulting 3D reconstruction map was improved from 4.1 Å to 3.7 Å resolution. The goCTF program is built on the open-source code of CTFFIND4, which adopts a consistent user interface for ease of use.

Fast multiscale reconstruction for Cryo-EM.

We present a multiscale reconstruction framework for single-particle analysis (SPA). The representation of three-dimensional (3D) objects with scaled basis functions permits the reconstruction of volumes at any desired scale in the real-space. This multiscale approach generates interesting opportunities in SPA for the stabilization of the initial volume problem or the 3D iterative refinement procedure. In particular, we show that reconstructions performed at coarse scale are more robust to angular errors and permit gains in computational speed. A key component of the proposed iterative scheme is its fast implementation. The costly step of reconstruction, which was previously hindering the use of advanced iterative methods in SPA, is formulated as a discrete convolution with a cost that does not depend on the number of projection directions. The inclusion of the contrast transfer function inside the imaging matrix is also done at no extra computational cost. By permitting full 3D regularization, the framework is by itself a robust alternative to direct methods for performing reconstruction in adverse imaging conditions (e.g., heavy noise, large angular misassignments, low number of projections). We present reconstructions obtained at different scales from a dataset of the 2015/2016 EMDataBank Map Challenge. The algorithm has been implemented in the Scipion package.

Sub-2\u2009\xc5 Ewald curvature corrected structure of an AAV2 capsid variant

Single-particle cryogenic electron microscopy (cryo-EM) provides a powerful methodology for structural biologists, but the resolutions typically attained with experimentally determined structures have lagged behind microscope capabilities. Here, we exploit several technical advances to improve resolution, including per-particle contrast transfer function (CTF) refinement and correction for Ewald sphere curvature. The latter is demonstrated with several experimental samples and should become more standard as resolutions increase or at lower microscope accelerating voltages. The combined application of the described methods to micrographs recorded on a Titan Krios enables structure determination at ~1.86-Å resolution of an adeno-associated virus serotype 2 variant (AAV2), an important gene-delivery vehicle. The resulting structural details provide an improved model for understanding the biology of AAV that will guide future vector development for gene therapy.