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IF 1.8 4区 工程技术 Q3 MICROSCOPY 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 Q3 MICROSCOPY 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 Q3 MICROSCOPY 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 Q3 MICROSCOPY 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
Reliable Electrochemical Setup for in situ Observations with an Atmospheric SEM. 可靠的电化学设置在现场观察与大气扫描电镜。
IF 1.8 4区 工程技术 Q3 MICROSCOPY Pub Date : 2022-06-11 DOI: 10.1093/jmicro/dfac028
Kaname Yoshida, Y. Sasaki, A. Kuwabara, Y. Ikuhara
A novel setup for the in situ observation of electrochemical reactions in liquids through atmospheric scanning electron microscopy is presented. The proposed liquid-phase electrochemical SEM system consists of a working electrode (WE) on an electrochemical chip (e-chip) and other two electrodes inserted into a liquid electrolyte; electrochemical reactions occurring at the WE are controlled precisely with an external potentiostat/galvanostat connected to the three electrodes. Copper deposition from a CuSO4 aqueous solution was conducted onto the WE, and simultaneous acquisition of nanoscale images and reliable electrochemical data was achieved with the proposed setup.
提出了一种利用大气扫描电子显微镜对液体中电化学反应进行原位观察的新装置。所提出的液相电化学SEM系统由电化学芯片(e-chip)上的一个工作电极(WE)和插入液体电解质中的另外两个电极组成;在WE发生的电化学反应是由连接到三个电极的外部恒电位器/恒流器精确控制的。将CuSO4水溶液中的铜沉积到WE上,利用该装置实现了纳米级图像和可靠的电化学数据的同时采集。
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引用次数: 0
Malaria Parasite Classification Framework using a Novel Channel Squeezed and Boosted CNN. 使用压缩和增强CNN的新频道的疟疾寄生虫分类框架。
IF 1.8 4区 工程技术 Q3 MICROSCOPY Pub Date : 2022-05-30 DOI: 10.1093/jmicro/dfac027
Dr. Saddam Hussain Khan, Najmus Saher Shah, Rabia Nuzhat, A. Majid, Hani Alquhayz, Asifullah Khan
Malaria is a life-threatening infection that infects the red blood cells (RBCs) that gradually grows throughout the body. The plasmodium parasite is caused by a female anopheles mosquito bite and severely affects numerous individuals within the world every year. Therefore, early detection tests are required to predict infected parasitic cells. The proposed technique exploits deep convolutional neural network (CNN) learning capability to detect the thin-blood smear parasitic patients from healthy individuals. In this regard, the detection is accomplished using a novel STM-SB-RENet block-based CNN that employs the idea of split-transform-merge (STM) and channel Squeezing-Boosting (SB) in a modified fashion. In this connection, a new convolutional block-based STM is developed, which systematically implements region and edge operations to explore the parasitic malaria pattern related to region-homogeneity, structural obstruction, and boundary-defining features. Moreover, the diverse boosted feature maps are achieved by incorporating the new channel SB and Transfer Learning (TL) idea in each STM block at abstract, intermediate, and target levels to capture minor contrast and texture variation between parasitic and normal artifacts. The malaria input images to the proposed models are initially transformed using discrete wavelet transform to generate enhanced and reduced feature space. The proposed architectures are validated using hold-out cross-validation on the National Institute of Health Malaria dataset. The proposed methods outperform the train from scratch, and TL-based fine-tuned existing techniques. The considerable performance (accuracy: 97.98%, sensitivity: 0.988, F-score: 0.980, and AUC: 0.996) of STM-SB-RENet suggests that it can be utilized to screen parasitic malaria patients.
疟疾是一种危及生命的感染,它会感染逐渐在全身生长的红细胞。疟原虫是由雌性按蚊叮咬引起的,每年都会严重影响世界上许多人。因此,需要进行早期检测测试来预测感染的寄生细胞。所提出的技术利用深度卷积神经网络(CNN)学习能力从健康个体中检测薄血涂片寄生虫患者。在这方面,检测是使用一种新的基于STM SB RENet块的CNN来完成的,该CNN以改进的方式采用了分割变换合并(STM)和信道压缩增强(SB)的思想。在这方面,开发了一种新的基于卷积块的STM,它系统地实现了区域和边缘运算,以探索与区域同质性、结构阻塞和边界定义特征相关的寄生疟疾模式。此外,通过在抽象、中间和目标级别将新的通道SB和转移学习(TL)思想结合到每个STM块中,以捕捉寄生和正常伪影之间的微小对比度和纹理变化,实现了不同的增强特征图。最初使用离散小波变换对所提出的模型的疟疾输入图像进行变换,以生成增强和缩小的特征空间。在国家卫生疟疾研究所数据集上使用保持交叉验证对所提出的架构进行了验证。所提出的方法优于从头开始的训练,以及基于TL的微调现有技术。STM-SB-RENet的显著性能(准确度:97.98%,灵敏度:0.988,F-评分:0.980,AUC:0.996)表明它可以用于筛查寄生虫疟疾患者。
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引用次数: 15
A Functional Platform for Remote use of Electron Microscopes Using Web Conferencing Systems. 基于Web会议系统的电子显微镜远程使用功能平台。
IF 1.8 4区 工程技术 Q3 MICROSCOPY Pub Date : 2022-05-26 DOI: 10.1093/jmicro/dfac026
Makoto Sugiura-Nakazato, Hiroshi Takase, Takeru Nakazato
In this study, we propose a useful system for remote sharing of transmission electron microscope (TEM) images by connecting three computers: a computer connected to a TEM, a computer distributing images, and a computer receiving images. Then, we confirmed the performance of three web conferencing systems, Microsoft Teams, Zoom, and Google Meet, to evaluate the usefulness of their remote use based on the clarity of images, smoothness of movement, and time lag in images on each computer in the system. A screen image can be captured using the following two methods: a virtual camera of a video distribution software that provided a good reaction speed to transfer images and the screen sharing by conference system software that could share high-quality images.
在这项研究中,我们提出了一个有用的系统,通过连接三台计算机来远程共享透射电子显微镜(TEM)图像:一台连接到TEM的计算机、一台分发图像的计算机和一台接收图像的计算机。然后,我们确认了三个网络会议系统的性能,即Microsoft Teams、Zoom和Google Meet,以根据系统中每台计算机上图像的清晰度、移动的流畅性和图像的时滞来评估其远程使用的有用性。屏幕图像可以使用以下两种方法拍摄:视频分发软件的虚拟相机提供了良好的反应速度来传输图像,以及会议系统软件共享屏幕,可以共享高质量的图像。
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引用次数: 0
Whole-cell observation of ZIO-stained Golgi apparatus in rat hepatocytes with serial block-face scanning electron microscope, SBF-SEM 用连续块面扫描电镜(sgf - sem)观察大鼠肝细胞zio染色高尔基体的全细胞变化
IF 1.8 4区 工程技术 Q3 MICROSCOPY Pub Date : 2022-05-10 DOI: 10.1093/jmicro/dfac024
K. Johkura, N. Usuda, Yoshihiro Tanaka, Motoaki Fukasawa, K. Murata, T. Noda, N. Ohno
Abstract The Golgi apparatus, which plays a role in various biosynthetic pathways, is usually identified in electron microscopy by the morphological criteria of lamellae. A 3-dimensional analyses with serial block-face scanning electron microscope (SBF-SEM), a volume-SEM proficient in obtaining large volumes of data at the whole-cell level, could be a promising technique for understanding the precise distribution and complex ultrastructure of Golgi apparatus, although optimal methods for such analyses remain unclear since the observation can be hampered with sample charging and low image contrast, and manual segmentation often requires significant manpower. The present study attempted the whole-cell observation and semi-automatic classification and segmentation of the Golgi apparatus in rat hepatocytes for the first time by SBF-SEM via ZIO staining, a classical osmium impregnation. The staining electron-densely visualized individual Golgi lamellae, and their ultrastructure could stably be observed without any noticeable charging. The simple thresholding of the serial images enabled the efficient reconstruction of the labeled Golgi apparatus, which revealed plural Golgi apparatus in one hepatocyte. The combination of the heavy metal-based histochemistry of zinc, iodine and osmium (ZIO) staining and SBF-SEM was useful in the 3-dimensional observation of the Golgi apparatus at the whole-cell level because of two technical advantages: (i) visualization of the Golgi apparatus without any heavy metal staining and efficient acquisition of the block-face images without additional conductive staining or any devices for eliminating charging; (ii) easy identification of the staining and hassle-free, semi-automatic classification and segmentation by simple thresholding of the images. This novel approach could elucidate the topographic characteristics of the Golgi apparatus in hepatocytes.
摘要高尔基体在各种生物合成途径中发挥作用,通常在电子显微镜下通过片层的形态学标准来鉴定。用连续块面扫描电子显微镜(SBF-SEM)进行三维分析,这是一种能够在全细胞水平上获得大量数据的体积SEM,可能是了解高尔基体精确分布和复杂超微结构的一种很有前途的技术,尽管这种分析的最佳方法仍然不清楚,因为观察可能会受到样本充电和低图像对比度的阻碍,并且手动分割通常需要大量人力。本研究首次尝试通过ZIO染色(一种经典的锇浸渍),通过SBF-SEM对大鼠肝细胞中的高尔基体进行全细胞观察和半自动分类和分割。染色电子致密地观察到单个高尔基体片层,其超微结构可以稳定地观察到,没有任何明显的电荷。序列图像的简单阈值化使得能够有效地重建标记的高尔基体,其揭示了一个肝细胞中的多个高尔基体。锌的基于重金属的组织化学的组合,碘和锇(ZIO)染色和SBF-SEM在整个细胞水平上对高尔基体的三维观察是有用的,因为有两个技术优势:(i)在没有任何重金属染色的情况下对高尔基物进行可视化,并且在没有额外的导电染色或任何用于消除充电的装置的情况下有效地获取块面图像;(ii)易于识别染色,并且通过图像的简单阈值进行无障碍的半自动分类和分割。这种新方法可以阐明肝细胞中高尔基体的地形特征。
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引用次数: 0
Design and Fabrication of an Electrochemical Chip for Liquid-Phase Transmission Electron Microscopy. 液相透射电镜电化学芯片的设计与制造。
IF 1.8 4区 工程技术 Q3 MICROSCOPY Pub Date : 2022-05-04 DOI: 10.1093/jmicro/dfac023
Y. Sasaki, Ayako Mizushima, Y. Mita, Kaname Yoshida, A. Kuwabara, Y. Ikuhara
Liquid-phase transmission electron microscopy (LP-TEM) can be used with an electrochemical chip (e-chip) to observe electrochemical reactions in a liquid in situ. The design of electrodes on an e-chip fabricated using microelectromechanical system (MEMS) technology cannot be easily changed. Here, we report a newly designed e-chip and its fabrication process. Electrodes with a desired shape were fabricated with various metals via an additional step of vacuum deposition onto our e-chip with a shadow mask. For precise control of the electrochemical reactions in LP-TEM, optimization of the electrode shape and material is critical.
液相透射电子显微镜(LP-TEM)可以与电化学芯片(e-chip)一起使用,原位观察液体中的电化学反应。使用微机电系统(MEMS)技术制造的电子芯片上的电极设计不容易改变。在此,我们报道了一种新设计的电子芯片及其制造工艺。通过使用荫罩在我们的电子芯片上进行额外的真空沉积步骤,用各种金属制造出具有所需形状的电极。为了精确控制LP-TEM中的电化学反应,电极形状和材料的优化至关重要。
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引用次数: 0
Feasibility of control of particle assembly by dielectrophoresis in liquid-cell transmission electron microscopy 液体细胞透射电子显微镜中介质电泳控制粒子组装的可行性
IF 1.8 4区 工程技术 Q3 MICROSCOPY Pub Date : 2022-04-23 DOI: 10.1093/jmicro/dfac021
T. Yamazaki, Hiromasa Niinomi, Y. Kimura
Abstract Liquid-cell transmission electron microscopy (LC-TEM) is a useful technique for observing phenomena in liquid samples with spatial and temporal resolutions similar to those of conventional transmission electron microscopy (TEM). This method is therefore expected to permit the visualization of phenomena previously inaccessible to conventional optical microscopy. However, dynamic processes such as nucleation are difficult to observe by this method because of difficulties in controlling the condition of the sample liquid in the observation area. To approach this problem, we focused on dielectrophoresis, in which electrodes are used to assemble particles, and we investigated the phenomena that occurred when an alternating-current signal was applied to an electrode in an existing liquid cell by using a phase-contrast optical microscope (PCM) and TEM. In PCM, we observed that colloidal particles in a solution were attracted to the electrodes to form assemblies, that the particles aligned along the electric field to form pearl chains and that the pearl chains accumulated to form colloidal crystals. However, these phenomena were not observed in the TEM study because of differences in the design of the relevant holders. The results of our study imply that the particle assembly by using dielectrophoretic forces in LC-TEM should be possible, but further studies, including electric device development, will be required to realize this in practice.
液池透射电子显微镜(LC-TEM)是一种有效的观察液体样品现象的技术,具有与传统透射电子显微镜(TEM)相似的空间和时间分辨率。因此,这种方法有望使以前传统光学显微镜无法实现的现象可视化。然而,由于难以控制观察区域内样品液体的状态,这种方法难以观察到成核等动态过程。为了解决这一问题,我们重点研究了用电极组装粒子的介电电泳,并利用相对比光学显微镜(PCM)和透射电镜(TEM)研究了将交流电流信号施加到现有液体电池中的电极上时发生的现象。在PCM中,我们观察到溶液中的胶体颗粒被吸引到电极上形成组件,颗粒沿着电场排列形成珍珠链,珍珠链积累形成胶体晶体。然而,由于相关支架设计的差异,在TEM研究中没有观察到这些现象。我们的研究结果表明,在LC-TEM中利用介电泳力进行粒子组装是可能的,但需要进一步的研究,包括电气设备的开发,才能在实践中实现这一点。
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引用次数: 2
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