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Fast computational approach with prior dimension reduction for three-dimensional chemical component analysis using CT data of spectral imaging. 利用光谱成像 CT 数据进行三维化学成分分析的先验降维快速计算方法。
IF 1.8 4区 工程技术 Q2 Medicine Pub Date : 2024-05-17 DOI: 10.1093/jmicro/dfae027
Motoki Shiga, Taisuke Ono, Kenichi Morishita, Keiji Kuno, Nanase Moriguchi
Spectral image (SI) measurement techniques, such as X-ray absorption fine structure (XAFS) imaging and scanning transmission electron microscopy (STEM) with energy-dispersive X-ray spectroscopy (EDS) or electron energy loss spectroscopy (EELS), are useful for identifying chemical structures in composite materials. Machine-learning techniques have been developed for automatic analysis of SI data, and their usefulness has been proven. Recently, an extended measurement technique combining SI with a computed tomography (CT) technique (CT-SI), such as CT-XAFS and STEM-EDS/EELS tomography, was developed to identify the three-dimensional (3D) structures of chemical components. CT-SI analysis can be conducted by combining CT reconstruction algorithms and chemical component analysis based on machine learning techniques. However, this analysis incurs high computational costs owing to the size of the CT-SI datasets. To address this problem, this study proposed a fast computational approach for 3D chemical component analysis in an unsupervised learning setting. The primary idea for reducing the computational cost involved compressing the CT-SI data prior to CT computation and performing 3D reconstruction and chemical component analysis on the compressed data. The proposed approach significantly reduced the computational cost without losing information about the 3D structure and chemical components. We experimentally evaluated the proposed approach using synthetic and real CT-XAFS data, which demonstrated that our approach achieved a significantly faster computational speed than the conventional approach while maintaining analysis performance. As the proposed procedure can be implemented with any CT algorithm, it is expected to accelerate 3D analyses with sparse regularized CT algorithms in noisy and sparse CT-SI datasets.
光谱图像(SI)测量技术,如 X 射线吸收精细结构(XAFS)成像和扫描透射电子显微镜(STEM)与能量色散 X 射线光谱(EDS)或电子能量损失光谱(EELS),对于确定复合材料中的化学结构非常有用。目前已开发出用于自动分析 SI 数据的机器学习技术,其实用性已得到证实。最近,一种将 SI 与计算机断层扫描(CT)技术(CT-SI)(如 CT-XAFS 和 STEM-EDS/EELS 断层扫描)相结合的扩展测量技术被开发出来,用于识别化学成分的三维(3D)结构。CT-SI 分析可通过结合 CT 重建算法和基于机器学习技术的化学成分分析来进行。然而,由于 CT-SI 数据集的大小,这种分析会产生很高的计算成本。为解决这一问题,本研究提出了一种在无监督学习环境下进行三维化学成分分析的快速计算方法。降低计算成本的主要思路是在 CT 计算之前压缩 CT-SI 数据,并在压缩数据上执行三维重建和化学成分分析。所提出的方法在不丢失三维结构和化学成分信息的情况下大大降低了计算成本。我们使用合成和真实的 CT-XAFS 数据对提出的方法进行了实验评估,结果表明我们的方法在保持分析性能的同时,计算速度明显快于传统方法。由于所提出的程序可以用任何 CT 算法来实现,因此有望在有噪声和稀疏的 CT-SI 数据集中加速稀疏正则化 CT 算法的三维分析。
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引用次数: 0
Spin polarization of photoelectrons emitted from spin-orbit coupled surface states of Pb/Ge(111). Pb/Ge(111) 自旋轨道耦合表面态发射的光电子的自旋极化。
IF 1.8 4区 工程技术 Q2 Medicine Pub Date : 2024-04-25 DOI: 10.1093/jmicro/dfae021
K. Yaji, Kenta Kuroda, Shunsuke Tsuda, Fumio Komori
We report that the spin vector of photoelectrons emitted from an atomic layer Pb grown on a germanium substrate [Pb/Ge(111)] can be controlled using an electric field of light. The spin polarization of photoelectrons excited by a linearly polarized light is precisely investigated by spin- and angle-resolved photoemission spectroscopy. The spin polarization of the photoelectrons observed in the mirror plane reverses between p- and s-polarized lights. Considering the dipole transition selection rule, the surface state of Pb/Ge(111) is represented by a linear combination of symmetric and asymmetric orbital components coupled with spins in mutually opposite directions. The spin direction of the photoelectrons is different from that of the initial state when the electric field vector of linearly polarized light deviates from p- or s-polarization conditions. The quantum interference in the photoexcitation process can determine the direction of the spin vector of photoelectrons.
我们报告了利用光的电场可以控制生长在锗基底 [Pb/Ge(111)] 上的原子层 Pb 发射的光电子的自旋矢量。利用自旋和角度分辨光发射光谱精确研究了线性偏振光激发的光电子的自旋极化。在镜面上观察到的光电子的自旋极化在 p 偏振光和 s 偏振光之间发生了逆转。考虑到偶极转换选择规则,Pb/Ge(111)的表面态由对称和非对称轨道成分的线性组合表示,它们的自旋方向相互相反。当线性偏振光的电场矢量偏离 p 偏振或 s 偏振条件时,光电子的自旋方向与初始状态不同。光激发过程中的量子干涉可以决定光电子自旋矢量的方向。
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引用次数: 0
Optimization of method for cross section hydrogels preparation using high-pressure freezing. 优化使用高压冷冻法制备横截面水凝胶的方法。
IF 1.8 4区 工程技术 Q2 Medicine Pub Date : 2024-04-24 DOI: 10.1093/jmicro/dfae020
Shuichi Ichihashi, Masahiko Kuwata, Kodai Kikuchi, Tatsushi Matsuyama, Akio Shimizu
High-pressure water freeze fracturing (HPWFF) is a method for preparing water-containing samples such as hydrogels for scanning electron microscopy, in which a sample is placed in a divisible pressure vessel, filled with water, sealed, frozen with liquid nitrogen, then vacuum dried after the vessel is divided. The pressure (about 200 MPa) generated by the phase transition from water to ice is expected to inhibit ice crystal formation that causes large deformation of microstructure in the sample. To maximize the useable sample size, where SEM observation is not affected by ice crystal growth, preparation conditions including the size of pressure vessel were examined in this work. Using pressure vessels 8.0 mm, 5.5 mm and 4.5 mm in diameter, agarose gel, gelatin gel, wheat starch hydrogel, wheat flour noodle and cellulose hydrogel were used to prepare SEM samples. With agarose gel, an area of 3.6 mm in diameter in the 5.5 mm vessel was achieved as the maximum size of the area observable without ice crystal growth. The observable size of other samples was comparable, except for gelatin gel. As a result, observation of the three-dimensional network structure of hydrogels could be performed over a wider range than with the conventional method without shredding or chemical treatment of the samples. Additionally, usability of agarose gel for sample support matrix in HPWFF was demonstrated.
高压水冷冻断裂法(HPWFF)是一种用于制备扫描电子显微镜所需的含水样品(如水凝胶)的方法,该方法是将样品置于可分割的压力容器中,注入水,密封,用液氮冷冻,然后在分割容器后进行真空干燥。从水到冰的相变所产生的压力(约 200 兆帕)有望抑制冰晶的形成,而冰晶的形成会导致样品微观结构的巨大变形。为了尽量增大可使用的样品尺寸,使 SEM 观察不受冰晶生长的影响,这项工作研究了包括压力容器尺寸在内的制备条件。使用直径分别为 8.0 毫米、5.5 毫米和 4.5 毫米的压力容器制备了琼脂糖凝胶、明胶、小麦淀粉水凝胶、小麦粉面条和纤维素水凝胶 SEM 样品。使用琼脂糖凝胶时,5.5 毫米容器中直径为 3.6 毫米的区域是在没有冰晶生长的情况下可观察到的最大区域。除明胶凝胶外,其他样品的可观察面积大小相当。因此,与传统方法相比,水凝胶三维网络结构的观测范围更广,无需粉碎样品或对样品进行化学处理。此外,还证明了在 HPWFF 中使用琼脂糖凝胶作为样品支撑基质的可行性。
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引用次数: 0
Diffraction contrast of ferroelectric domains in DPC STEM images. DPC STEM 图像中铁电畴的衍射对比。
IF 1.8 4区 工程技术 Q2 Medicine Pub Date : 2024-04-17 DOI: 10.1093/jmicro/dfae019
Masaya Takamoto, T. Seki, Y. Ikuhara, Naoya Shibata
Differential phase contrast scanning transmission electron microscopy (DPC STEM) is a powerful technique for directly visualizing electromagnetic fields inside materials at high spatial resolution. Electric field observation within ferroelectric materials is potentially possible by DPC STEM, but concomitant diffraction contrast hinders the quantitative electric field evaluation. Diffraction contrast is basically caused by the diffraction-condition variation inside a field-of-view, but in the case of ferroelectric materials, the diffraction conditions can also change with respect to the polarization orientations. To quantitatively observe electric field distribution inside ferroelectric domains, the formation mechanism of diffraction contrast should be clarified in detail. In this study, we systematically simulated diffraction contrast of ferroelectric domains in DPC STEM images based on the dynamical diffraction theory, and clarify the issues for quantitatively observing electric fields inside ferroelectric domains. Furthermore, we conducted experimental DPC STEM observations for a ferroelectric material to confirm the influence of diffraction contrast predicted by the simulations.
差相对比扫描透射电子显微镜(DPC STEM)是一种强大的技术,可直接以高空间分辨率观察材料内部的电磁场。DPC STEM 有可能观察到铁电材料内部的电场,但随之而来的衍射对比阻碍了电场的定量评估。衍射对比度基本上是由视场内的衍射条件变化引起的,但在铁电材料中,衍射条件也会随极化方向的变化而变化。要定量观测铁电畴内的电场分布,就必须详细阐明衍射对比的形成机制。本研究基于动态衍射理论,系统模拟了 DPC STEM 图像中铁电畴的衍射对比,并阐明了定量观测铁电畴内部电场的问题。此外,我们还对一种铁电材料进行了 DPC STEM 实验观测,以证实模拟预测的衍射对比度的影响。
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引用次数: 0
Correction to: Electron holography observation of electron spin polarization around charged insulating wire. 更正:带电绝缘线周围电子自旋极化的电子全息观测。
IF 1.8 4区 工程技术 Q2 Medicine Pub Date : 2024-04-11 DOI: 10.1093/jmicro/dfae014
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引用次数: 0
Editorial: In-situ microscopy. 社论:原位显微镜。
IF 1.8 4区 工程技术 Q2 Medicine Pub Date : 2024-04-01 DOI: 10.1093/jmicro/dfae006
Toshie Yaguchi, Ayako Hashimoto, Junko Matsuda
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引用次数: 0
In This Issue 本期报道
IF 1.8 4区 工程技术 Q2 Medicine Pub Date : 2023-08-01 DOI: 10.1093/jmicro/dfad038
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引用次数: 0
Real-time scanning electron microscopy of unfixed tissue in the solution using a deformable and electron-transmissive film 使用可变形和电子透射膜对溶液中未固定组织进行实时扫描电子显微镜检查
IF 1.8 4区 工程技术 Q2 Medicine Pub Date : 2022-06-17 DOI: 10.1093/jmicro/dfac030
Seine A. Shintani, S. Yamaguchi, H. Takadama
Abstract It is difficult to use scanning electron microscopy to observe the structure and movement of biological tissue immersed in the solution. To enable such observations, we created a highly deformable and electron-transmissive polyimide film that can withstand the pressure difference between the high-vacuum electron column and the atmospheric-pressure sample chamber. With this film, we used scanning electron microscopy to measure the intrinsic fine structure and movement of the contractile fibers of excised mouse heart immersed in physiological solutions. Our measurements revealed that the excised heart is a dynamic tissue that undergoes relaxation oscillation based on a three-dimensional force balance.
摘要用扫描电子显微镜很难观察浸泡在溶液中的生物组织的结构和运动。为了进行这样的观察,我们制作了一种高度可变形和电子透射的聚酰亚胺薄膜,它可以承受高真空电子柱和大气压样品室之间的压力差。利用这种薄膜,我们使用扫描电子显微镜测量了浸泡在生理溶液中的离体小鼠心脏收缩纤维的内在精细结构和运动。我们的测量结果表明,切除的心脏是一个动态组织,基于三维力平衡进行松弛振荡。
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引用次数: 0
Atomic-Resolution STEM Image Denoising by Total Variation Regularization. 基于全变分正则化的原子分辨率STEM图像去噪。
IF 1.8 4区 工程技术 Q2 Medicine Pub Date : 2022-06-17 DOI: 10.1093/jmicro/dfac032
Kazuaki Kawahara, R. Ishikawa, Shun Sasano, N. Shibata, Y. Ikuhara
Atomic-resolution electron microscopy imaging of solid state material is a powerful method for structural analysis. Scanning transmission electron microscopy (STEM) is one of the actively used techniques to directly observe atoms in materials. However, some materials are easily damaged by the electron beam irradiation, and only noisy images are available when we decrease the electron dose to avoid beam damages. Therefore, a denoising process is necessary for precise structural analysis in low-dose STEM. In this study, we propose total variation (TV) denoising algorithm to remove quantum noise in a STEM image. We defined an entropy of STEM image that corresponds to the image contrast to determine a hyperparameter and we found that there is a hyperparameter that maximize the entropy. We acquired atomic resolution STEM image of CaF2 viewed along the [001] direction, and executed TV denoising. The atomic columns of Ca and F are clearly visualized by the TV denoising, and atomic position of Ca and F are determined with the error of ± 1 pm and ± 4 pm, respectively.
固体材料的原子分辨率电子显微镜成像是结构分析的一种强大方法。扫描透射电子显微镜(STEM)是直接观察材料中原子的一种常用技术。然而,一些材料很容易被电子束辐照损坏,当我们减少电子剂量以避免电子束损坏时,只有噪声图像可用。因此,对于低剂量STEM中的精确结构分析,去噪过程是必要的。在这项研究中,我们提出了全变分(TV)去噪算法来去除STEM图像中的量子噪声。我们定义了STEM图像的熵,该熵对应于图像对比度以确定超参数,并且我们发现存在使熵最大化的超参数。我们获得了沿[001]方向观察的CaF2的原子分辨率STEM图像,并执行了TV去噪。通过TV去噪,Ca和F的原子柱被清晰地可视化,Ca和F的原子位置被确定,误差分别为±1pm和±4pm。
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引用次数: 4
Super-Resolution Reconstruction Based on BM3D and Compressed Sensing. 基于BM3D和压缩感知的超分辨率重建。
IF 1.8 4区 工程技术 Q2 Medicine Pub Date : 2022-06-16 DOI: 10.1093/jmicro/dfac029
Cheng Tao, Dongdong Jia
In the various papers published in the field of super-resolution microscopy, denoising of raw images based on Block-matching and 3D filtering (BM3D) was rarely reported. BM3D for blocks of different sizes was studied. The denoising ability is related to block sizes. The larger the block is, the better the denoising effect is. When the block size is bigger than 40, the good denoising effect can be achieved. Denoising has great influence on the super-resolution reconstruction effect and the reconstruction time. Better super-resolution reconstruction and shorter reconstruction time can be achieved after denoising. Using compressed sensing, only 20 raw images are needed for super-resolution reconstruction. The temporal resolution is less than half a second. The spatial resolution is also greatly improved.
在超分辨率显微镜领域发表的各种论文中,很少报道基于块匹配和三维滤波(BM3D)的原始图像去噪。研究了不同尺寸块体的BM3D。去噪能力与块大小有关。块越大,去噪效果越好。当块大小大于40时,可以获得良好的去噪效果。去噪对超分辨率重建效果和重建时间有很大影响。去噪后可以获得更好的超分辨率重建和更短的重建时间。使用压缩传感,超分辨率重建只需要20张原始图像。时间分辨率不到半秒。空间分辨率也大大提高。
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引用次数: 0
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Microscopy
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