Determination of the illuminating angle and defocus spread in transmission electron microscopy

In high resolution electron microscopy the beam divergence and defocus spread are important factors determining the resolution limit of the microscope. In this paper a straightforward method is proposed to estimate the illuminating angle (beam divergence) and the parameter of defocus spread using optical diffraction patterns from a through focal series of electron micrographs of a thin amorphous film.     

Automatic selection of molecular images from dark field electron micrographs

A method is described which can be used objectively to select putative molecular images from dark field electron micrographs of unstained molecules. The only characteristic of the molecule required for automatic selection is an estimate of molecular weight. Structures are selected from micrographs by a series of steps including: low pass filtering, edge detection and mass determination. The procedure is shown to be reliable for images with signal-to-noise ratios of at least 4.0. Moreover, the method is insensitive to both the shape and the number of molecules in the image. Five different molecules with molecular weights between MW 330,000 and MW 4000 are successfully selected from low dose STEM and high dose tilt beam dark field electron micrographs.     

An overview of state‐of‐the‐art image restoration in electron microscopy

In Life Science research, electron microscopy (EM) is an essential tool for morphological analysis at the subcellular level as it allows for visualization at nanometer resolution. However, electron micrographs contain image degradations such as noise and blur caused by electromagnetic interference, electron counting errors, magnetic lens imperfections, electron diffraction, etc. These imperfections in raw image quality are inevitable and hamper subsequent image analysis and visualization. In an effort to mitigate these artefacts, many electron microscopy image restoration algorithms have been proposed in the last years. Most of these methods rely on generic assumptions on the image or degradations and are therefore outperformed by advanced methods that are based on more accurate models. Ideally, a method will accurately model the specific degradations that fit the physical acquisition settings. In this overview paper, we discuss different electron microscopy image degradation solutions and demonstrate that dedicated artefact regularisation results in higher quality restoration and is applicable through recently developed probabilistic methods.     

运用模块化方法建立口腔修复有限元模型

以工程领域中的模块化方法为核心建立了牙颌组织的有限元模型库。对标本进行CT扫描、数据提取、和三维重建技术建立牙颌组织的实体模型。对实体模型切分模块 ,得到一套正常牙列的模块化模型库 ,并在其基础上派生一系列反映上下颌牙生理、病理情况的模型库。上述方法可建成正常牙、牙槽骨不同程度吸收、牙周不同程度松动、缺牙区牙槽骨、固定桥修复体、可摘局部义齿修复体等有限元模型。将模块化设计与有限元方法相结合 ,可高效地生成适用于口腔修复学设计和分析的有限元模型库。     

Improved high resolution image processing of bright field electron micrographs: II. Experiment

The new methods of nonlinear image processing are applied to high resolution experimental micrographs of chlorinated copper phthalocyanine taken on the Kyoto 500 kV electron microscope. With these new methods of image processing the phase and amplitude of the specimen transmission function are reconstructed from a defocus series of conventional transmission electron micrographs (bright field). Strong scattering, partial coherence and statistical noise have been included. Both of these new methods are based on the MAP (maximum a posteriori) criterion generalized to include reconstruction from multiple input images. In a companion paper (the first part of this two-part report) the theory behind these methods was presented and in this paper it is tested on actual experimental micrographs. A significant increase in resolution has been obtained with computer image processing. The point-to-point resolution obtained here with computer image processing of 500 kV electron micrographs is of the order of 1.2–1.4 Å which represents a 30–50% increase in resolution.     

不确定声场分析的区间矩阵分解摄动有限元法

针对修正一阶区间摄动有限元法存在的一阶Taylor展开误差较大和求解摄动逆矩阵时计算效率不高的缺陷,提出区间矩阵分解摄动有限元法(Decomposed interval matrix perturbation finite element method, DIMPFEM)。该方法将系统动态刚度矩阵分解为若干系统子矩阵之和,每个系统子矩阵的摄动矩阵用摄动因子和常量矩阵的乘积表示,避免了摄动矩阵的Taylor展开误差;采用Epsilon算法求解摄动逆矩阵的修正Neumann级数,有效提高了计算效率。将DIMPFEM应用于具有区间参数的二维管道和二维商务车声腔模型的声压响应分析,分析结果表明,与修正一阶区间摄动有限元法比较,DIMPFEM获得了更高的计算精度和计算效率。     

Generalized approach for accelerated maximum likelihood based image restoration applied to three-dimensional fluorescence microscopy

For deconvolution applications in three-dimensional microscopy we derived and implemented a generic, accelerated maximum likelihood image restoration algorithm. A conjugate gradient iteration scheme was used considering either Gaussian or Poisson noise models. Poisson models are better suited to low intensity fluorescent image data; typically, they show smaller restoration errors and smoother results. For the regularization, we modified the standard Tikhonov method. However, the generic design of the algorithm allows for more regularization approaches. The Hessian matrix of the restoration functional was used to determine the step size. We compared restoration error and convergence behaviour between the classical line-search and the Hessian matrix method. Under typical working conditions, the restoration error did not increase over that of the line-search and the speed of convergence did not significantly decrease allowing for a twofold increase in processing speed. To determine the regularization parameter, we modified the generalized cross-validation method. Tests that were done on both simulated and experimental fluorescence wide-field data show reliable results.     

改进的奇异值分解法估计图像点扩散函数

为了提高图像复原算法的性能,提出了一种改进的奇异值分解法估计图像的点扩散函数。从图像的退化离散模型出发,对图像进行逐层分块奇异值分解,并自动选取奇异值重组阶数以减少噪声对估计的影响。利用理想图像奇异值向量平均能谱指数模型,估计点扩散函数奇异值向量的频谱,再反傅里叶变换得到其时域结果。实验结果表明,该方法能在不同信噪比情况下估计成像系统的点扩散函数,估计结果比原有估计方法有所提高,有望为图像复原算法的预处理提供一种有效的手段。     

Three-dimensional reconstruction of biological macromolecular complexes from in-lens scanning electron micrographs

Two helical samples: F-actin and the bacteriophage T4 tail sheath were reconstructed in three dimensions from contrast enhanced (rotational shadowing and negatively stained) in-lens cryo-field emission scanning electron micrographs, using the iterative real-space helical reconstruction method. The F-actin – and bacteriophage T4 reconstructions compare favourably to an atomic model refined against fibre diffraction data and a cryo-electron microscopy reconstruction, respectively. These results show that single-particle methods, developed for macromolecules imaged in the transmission electron microscope can be applied to cryo-field emission scanning electron micrographs data with appropriate symmetry.     

Increased depth of field and stereo pairs of fluorescence micrographs via inverse filtering and maximum-likelihood estimation

Image processing methods are presented for effectively increasing the depth of field and for generating stereo pairs of fluorescence micrographs from a conventional optical microscope. In developing these methods the slice theorem of computed tomography is used. In this way the image reconstruction problem is reduced to one of processing only two-dimensional arrays rather than three-dimensional arrays and the classical difficult problem of restoring missing Fourier components within the missing cone region is circumvented. Two different approaches to such processing are presented. One approach is based on inverse filtering. Another approach is based on previous development of iterative image restoration algorithms for quantum-limited incoherent imagery, founded on maximum-likelihood estimation. Limited experimentation with real micrographs shows that both approaches work well. Some preliminary comparisons are made between the different variations of the methods tested, which point out the advantages and present limitations. Both methods can be implemented on IBM-AT-compatible computers with relatively fast execution times. Advantages that these methods have over confocal microscopy are (i) the optical and computing equipment required is less expensive, and (ii) a conventional microscope when set up properly can have much better light sensitivity than a confocal microscope.     

修正的差分进化算法在系统可靠性中的应用

提出了一种修正的差分进化算法(MDE)以解决4种系统可靠性问题,它们分别为串联系统、复杂(桥)系统、串并联系统和超速保护系统.MDE算法对DE算法的变异操作进行了一种有效的改进,使得所有解向量以递增的概率朝全局最优解方向移动.另外,罚函数法被用来处理目标函数值和资源约束之间的关系.相应地,通过结合MDE算法和罚函数法以获得令人满意的可行解.实验结果表明,MDE算法所获得的4种系统的可靠性都要好于文献中所报道的结果,分别为0.931 682、0.999 889 63、0.999 976 65和0.999 955.     

A new method for the determination of the wave aberration function for high resolution TEM 1. Measurement of the symmetric aberrations

A new method for the accurate determination of the symmetric coefficients of the wave aberration function has been developed. The relative defoci and displacements of images in a focus series are determined from an analysis of the phase correlation function between pairs of images, allowing the restoration of an image wave even when focus and specimen drift are present. Subsequently, the absolute coefficients of both defocus and 2-fold astigmatism are determined with a phase contrast index function. Overall this method allows a very accurate automated aberration determination even for largely crystalline samples with little amorphous contamination. Using experimental images of the complex oxide Nb16W18O94 we have demonstrated the new method and critically compared it with existing diffractogram based aberration determinations. A series of protocols for practical implementation is also given together with a detailed analysis of the accuracy achieved. Finally a focal series restoration of Nb16W18O94 with symmetric aberrations determined automatically using this method is presented.     

Simulation of annular dark field stem images using a modified multislice method

The multislice method of image simulation has been extensively applied to conventional transmission electron micrographs (CTEM), but not yet to scanning transmission electron micrographs (STEM). In this paper the multislice method is adapted for application to the STEM and several examples relevant to the VG-HB501 STEM are presented. Annular dark field images of a (111) crystal silicon substrate supporting a single heavy atom are calculated.     

Fabrication of semi-transparent super-hydrophobic surface based on silica hierarchical structures

This study successfully develops a versatile method of producing superhydrophobic surfaces with micro/nano-silica hierarchical structures on glass surfaces. Optically transparent super hydrophobic silica thin films were prepared by spin-coating silica particles suspended in a precursor solution of silane, ethanol, and H₂O with molar ratio of 1:4:4. The resulting super hydrophobic films were characterized by scanning electron microscopy (SEM), optical transmission, and contact angle measurements. The glass substrates in this study were modified with different particles: micro-silica particles, nano-silica particles, and hierarchical structures. This study includes SEM micrographs of the modified glass surfaces with hierarchical structures at different magnifications.     

Three-dimensional view of the chromatin in freeze-fractured chicken erythrocyte nuclei.

The freeze-fracture thaw-fix (FfTF) technique described in earlier papers is applied in the present work to more detailed study of the chicken erythrocyte, by transmission replicas and high resolution scanning electron microscopy (3 nm scan beam size). The three-dimensional structure of the chromatin, and possibly the non-histone protein matrix, of fractured nuclei is to a large extent retained in this method of preparation and seen in stereomicrographs. In these micrographs the helical sub-structure of the 25 nm chromatin strands can be seen at about the same resolution as that of previously published micrographs in which extracted chromatin is viewed by negative contrast or after metal shadowing. The useful resolution of the secondary electron micrographs, for a suitably mounted specimen, is shown to be as good as that of transmission micrographs of platinum-carbon replicas of the same material.     

Identification of the three-dimensional gel microstructure from transmission electron micrographs

Mass transport in gels depends crucially on local properties of the gel network. We propose a method for identifying the three‐dimensional (3D) gel microstructure from statistical information in transmission electron micrographs. The gel strand network is modelled as a random graph with nodes and edges (branches). The distribution of edge length, the number of edges at nodes and the angles between edges at a node are estimated from transmission electron micrographs by image analysis methods. The 3D network is simulated by Markov chain Monte Carlo, with a probability function based on the statistical information found from the micrographs. The micrographs are projections of stained gel strands in slices, and we derive a formula for estimating the thickness of the stained gel slice based on the total projected gel strand length and the number of times that gel strands enter or exit the slice.     

空间目标图像的非凸稀疏正则化波后复原

现有的空间目标图像波后处理方法多直接套用自然光学图像的复原技术,效果并不理想。本文通过分析空间目标图像的近似稀疏性和灰度值服从超拉普拉斯分布的独有特点,提出了一个采用正则化方法的非凸稀疏正则化空间目标图像复原模型。在数值计算过程中,根据交替方向乘数法将复原模型分解为两个子问题,对凸优化子问题采用快速傅里叶变换求解,对非凸优化子问题采用固定点迭代方法求解。文中设计了非凸稀疏正则化空间目标图像波后复原的完整算法流程,并针对模拟图像和真实空间目标图像进行了对比验证。结果显示:相对于最近的流行算法,提出方法的最大峰值信噪比提高了2dB,最大平均结构相似度提高了0.17,最大信息熵提高了3.85,图像清晰度提高了2.65。     

A simple,combined diffractometer and scanning microdensitometer

A simple device for densitometering electron micrographs or other transparencies by one-dimensional scanning is described. Micrographs of crystalline materials are oriented by means of their optical diffraction patterns displayed with a slightly modified microscope.     

修正时序法在石化装置数据校正中的应用研究

为了有效地克服传统统计检验和线性化处理方法进行过失误差侦破、数据校正与参数估计时存在的局限性，对现有过程测量数据校正技术进行了综合分析，探讨了数据分类、过失误差侦破和过程测量数据校正等问题，以具有代表性的化工装置和炼油装置为研究对象，提出了修正时间序列分析法，给出了时间序列分析法的基本思想、概率模型和特点，以及含随机误差的数据校正方法，并将时序法用于过失误差侦破。在大型化工装置的测量数据校正结果表明，该方法是实用性强、方便有效的数据校正新策略。