A Ishizuka;K Ishizuka;R Ishikawa;N Shibata;Y Ikuhara;H Hashiguchi;R Sagawa
Although the possibility of locating single atom in three dimensions using the scanning transmission electron microscope (STEM) has been discussed with the advent of aberration correction technology, it is still a big challenge. In this report we have developed deconvolution routines based on maximum entropy method (MEM) and Richardson–Lucy algorithm (RLA), which are applicable to the STEM-annular dark-field (ADF) though-focus images to improve the depth resolution. The new three-dimensional (3D) deconvolution routines require a limited defocus-range of STEM-ADF images that covers a whole sample and some vacuum regions. Since the STEM-ADF probe is infinitely elongated along the optical axis, a 3D convolution is performed with a two-dimensional (2D) convolution over xy-plane using the 2D fast Fourier transform in reciprocal space, and a one-dimensional convolution along the z-direction in real space. Using our new deconvolution routines, we have processed simulated focal series of STEM-ADF images for single Ce dopants embedded in wurtzite-type AlN. Applying the MEM, the Ce peaks are clearly localized along the depth, and the peak width is reduced down to almost one half. We also applied the new deconvolution routines to experimental focal series of STEM-ADF images of a monolayer graphene. The RLA gives smooth and high-P/B ratio scattering distribution, and the graphene layer can be easily detected. Using our deconvolution algorithms, we can determine the depth locations of the heavy dopants and the graphene layer within the precision of 0.1 and 0.2 nm, respectively. Thus, the deconvolution must be extremely useful for the optical sectioning with 3D STEM-ADF images.
{"title":"Improving the depth resolution of STEM-ADF sectioning by 3D deconvolution","authors":"A Ishizuka;K Ishizuka;R Ishikawa;N Shibata;Y Ikuhara;H Hashiguchi;R Sagawa","doi":"10.1093/jmicro/dfaa056","DOIUrl":"10.1093/jmicro/dfaa056","url":null,"abstract":"Although the possibility of locating single atom in three dimensions using the scanning transmission electron microscope (STEM) has been discussed with the advent of aberration correction technology, it is still a big challenge. In this report we have developed deconvolution routines based on maximum entropy method (MEM) and Richardson–Lucy algorithm (RLA), which are applicable to the STEM-annular dark-field (ADF) though-focus images to improve the depth resolution. The new three-dimensional (3D) deconvolution routines require a limited defocus-range of STEM-ADF images that covers a whole sample and some vacuum regions. Since the STEM-ADF probe is infinitely elongated along the optical axis, a 3D convolution is performed with a two-dimensional (2D) convolution over xy-plane using the 2D fast Fourier transform in reciprocal space, and a one-dimensional convolution along the z-direction in real space. Using our new deconvolution routines, we have processed simulated focal series of STEM-ADF images for single Ce dopants embedded in wurtzite-type AlN. Applying the MEM, the Ce peaks are clearly localized along the depth, and the peak width is reduced down to almost one half. We also applied the new deconvolution routines to experimental focal series of STEM-ADF images of a monolayer graphene. The RLA gives smooth and high-P/B ratio scattering distribution, and the graphene layer can be easily detected. Using our deconvolution algorithms, we can determine the depth locations of the heavy dopants and the graphene layer within the precision of 0.1 and 0.2 nm, respectively. Thus, the deconvolution must be extremely useful for the optical sectioning with 3D STEM-ADF images.","PeriodicalId":18515,"journal":{"name":"Microscopy","volume":"70 1","pages":"241-249"},"PeriodicalIF":1.8,"publicationDate":"2020-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/jmicro/dfaa056","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38484133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We have designed and evaluated a cryo-electron microscopy (cryo-EM) system for higher-resolution single particle analysis and high-precision electron 3D crystallography. The system comprises a JEOL CRYO ARM 300 electron microscope—the first machine of this model—and a direct detection device camera, a scintillator-coupled camera, GPU clusters connected with a camera control computer and software for automated-data collection and efficient and accurate operation. The microscope provides parallel illumination of a highly coherent 300-kV electron beam to a sample from a cold-field emission gun and filters out energy-loss electrons through the sample with an in-column energy filter. The gun and filter are highly effective in improving imaging and diffraction, respectively, and have provided high quality data since July 2018. We here report on the characteristics of the cryo-EM system, updates, our progress and future plan for running such cryo-EM machines in RIKEN SPring-8 Center.
我们设计并评估了一种用于更高分辨率单粒子分析和高精度电子3D结晶学的冷冻电子显微镜(cryo-EM)系统。该系统包括一台JEOL CRYO ARM 300电子显微镜——该型号的第一台机器——以及一台直接检测设备相机、一台闪烁体耦合相机、与相机控制计算机连接的GPU集群和用于自动数据收集和高效准确操作的软件。该显微镜从冷场发射枪向样品提供高度相干的300kV电子束的平行照明,并用柱内能量过滤器过滤掉通过样品的能量损失电子。该枪和滤波器分别在改善成像和衍射方面非常有效,自2018年7月以来提供了高质量的数据。我们在这里报道了冷冻电镜系统的特点、更新、我们的进展以及在理研SPring-8中心运行这种冷冻电镜机器的未来计划。
{"title":"Advances in cryo-EM and ED with a cold-field emission beam and energy filtration —Refinements of the CRYO ARM 300 system in RIKEN SPring-8 center—","authors":"Saori Maki-Yonekura;Tasuku Hamaguchi;Hisashi Naitow;Kiyofumi Takaba;Koji Yonekura","doi":"10.1093/jmicro/dfaa052","DOIUrl":"10.1093/jmicro/dfaa052","url":null,"abstract":"We have designed and evaluated a cryo-electron microscopy (cryo-EM) system for higher-resolution single particle analysis and high-precision electron 3D crystallography. The system comprises a JEOL CRYO ARM 300 electron microscope—the first machine of this model—and a direct detection device camera, a scintillator-coupled camera, GPU clusters connected with a camera control computer and software for automated-data collection and efficient and accurate operation. The microscope provides parallel illumination of a highly coherent 300-kV electron beam to a sample from a cold-field emission gun and filters out energy-loss electrons through the sample with an in-column energy filter. The gun and filter are highly effective in improving imaging and diffraction, respectively, and have provided high quality data since July 2018. We here report on the characteristics of the cryo-EM system, updates, our progress and future plan for running such cryo-EM machines in RIKEN SPring-8 Center.","PeriodicalId":18515,"journal":{"name":"Microscopy","volume":"70 1","pages":"232-240"},"PeriodicalIF":1.8,"publicationDate":"2020-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/jmicro/dfaa052","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38647638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We describe small-angle electron diffraction (SmAED) and Lorentz microscopy using a conventional transmission electron microscope. In SmAED, electron diffraction patterns with a wide-angular range on the order of 1 × 10 −2