{"title":"Fast computational approach with prior dimension reduction for three-dimensional chemical component analysis using CT data of spectral imaging.","authors":"Motoki Shiga, Taisuke Ono, Kenichi Morishita, Keiji Kuno, Nanase Moriguchi","doi":"10.1093/jmicro/dfae027","DOIUrl":"https://doi.org/10.1093/jmicro/dfae027","url":null,"abstract":"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.","PeriodicalId":48655,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140966117","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}
MicroscopyPub Date : 2024-04-25DOI: 10.1093/jmicro/dfae021
K. Yaji, Kenta Kuroda, Shunsuke Tsuda, Fumio Komori
{"title":"Spin polarization of photoelectrons emitted from spin-orbit coupled surface states of Pb/Ge(111).","authors":"K. Yaji, Kenta Kuroda, Shunsuke Tsuda, Fumio Komori","doi":"10.1093/jmicro/dfae021","DOIUrl":"https://doi.org/10.1093/jmicro/dfae021","url":null,"abstract":"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.","PeriodicalId":48655,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140656667","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}
{"title":"Optimization of method for cross section hydrogels preparation using high-pressure freezing.","authors":"Shuichi Ichihashi, Masahiko Kuwata, Kodai Kikuchi, Tatsushi Matsuyama, Akio Shimizu","doi":"10.1093/jmicro/dfae020","DOIUrl":"https://doi.org/10.1093/jmicro/dfae020","url":null,"abstract":"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.","PeriodicalId":48655,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140665050","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}
MicroscopyPub Date : 2024-04-17DOI: 10.1093/jmicro/dfae019
Masaya Takamoto, T. Seki, Y. Ikuhara, Naoya Shibata
{"title":"Diffraction contrast of ferroelectric domains in DPC STEM images.","authors":"Masaya Takamoto, T. Seki, Y. Ikuhara, Naoya Shibata","doi":"10.1093/jmicro/dfae019","DOIUrl":"https://doi.org/10.1093/jmicro/dfae019","url":null,"abstract":"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.","PeriodicalId":48655,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140693104","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}
MicroscopyPub Date : 2024-04-11DOI: 10.1093/jmicro/dfae014
{"title":"Correction to: Electron holography observation of electron spin polarization around charged insulating wire.","authors":"","doi":"10.1093/jmicro/dfae014","DOIUrl":"https://doi.org/10.1093/jmicro/dfae014","url":null,"abstract":"","PeriodicalId":48655,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140713942","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}
MicroscopyPub Date : 2023-08-01DOI: 10.1093/jmicro/dfad038
{"title":"In This Issue","authors":"","doi":"10.1093/jmicro/dfad038","DOIUrl":"https://doi.org/10.1093/jmicro/dfad038","url":null,"abstract":"","PeriodicalId":48655,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42276181","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}
MicroscopyPub Date : 2022-06-17DOI: 10.1093/jmicro/dfac030
Seine A. Shintani, S. Yamaguchi, H. Takadama
{"title":"Real-time scanning electron microscopy of unfixed tissue in the solution using a deformable and electron-transmissive film","authors":"Seine A. Shintani, S. Yamaguchi, H. Takadama","doi":"10.1093/jmicro/dfac030","DOIUrl":"https://doi.org/10.1093/jmicro/dfac030","url":null,"abstract":"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.","PeriodicalId":48655,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2022-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48209000","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}
MicroscopyPub Date : 2022-06-17DOI: 10.1093/jmicro/dfac032
Kazuaki Kawahara, R. Ishikawa, Shun Sasano, N. Shibata, Y. Ikuhara
{"title":"Atomic-Resolution STEM Image Denoising by Total Variation Regularization.","authors":"Kazuaki Kawahara, R. Ishikawa, Shun Sasano, N. Shibata, Y. Ikuhara","doi":"10.1093/jmicro/dfac032","DOIUrl":"https://doi.org/10.1093/jmicro/dfac032","url":null,"abstract":"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.","PeriodicalId":48655,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2022-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48967934","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}
MicroscopyPub Date : 2022-06-16DOI: 10.1093/jmicro/dfac029
Cheng Tao, Dongdong Jia
{"title":"Super-Resolution Reconstruction Based on BM3D and Compressed Sensing.","authors":"Cheng Tao, Dongdong Jia","doi":"10.1093/jmicro/dfac029","DOIUrl":"https://doi.org/10.1093/jmicro/dfac029","url":null,"abstract":"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.","PeriodicalId":48655,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2022-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42706213","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}