Microscopy最新文献

{"title":"Preliminary study of improved median filter using adaptively mask size in light microscopic image","authors":"Ji-Youn Kim;Youngjin Lee","doi":"10.1093/jmicro/dfz111","DOIUrl":"10.1093/jmicro/dfz111","url":null,"abstract":"This study aimed to develop and evaluate an improved median filter (IMF) with an adaptive mask size for light microscope (LM) images. We acquired images of the mouse first molar using a LM at 100× magnification. The images obtained using our proposed IMF were compared with those from a conventional median filter. Several parameters such as the contrast-to-noise ratio, coefficient of variation, no-reference assessments and peak signal-to-noise ratio were employed to evaluate the image quality quantitatively. The results demonstrated that the proposed IMF could effectively de-noise the LM images and preserve the image details, achieving a better performance than the conventional median filter. This study discusses evaluation of an improved median fi lter with an adaptive mask size for light microscope (LM) images. The results demonstrated that the proposed fi lter could effectively denoise the LM images and preserve the image details, achieving a better performance than the conventional median fi lter.","PeriodicalId":18515,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/jmicro/dfz111","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37679187","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":"Visualization of different carrier concentrations in n-type-GaN semiconductors by phase-shifting electron holography with multiple electron biprisms","authors":"Kazuo Yamamoto;Kiyotaka Nakano;Atsushi Tanaka;Yoshio Honda;Yuto Ando;Masaya Ogura;Miko Matsumoto;Satoshi Anada;Yukari Ishikawa;Hiroshi Amano;Tsukasa Hirayama","doi":"10.1093/jmicro/dfz037","DOIUrl":"10.1093/jmicro/dfz037","url":null,"abstract":"Phase-shifting electron holography (PS-EH) using a transmission electron microscope (TEM) was applied to visualize layers with different concentrations of carriers activated by Si (at dopant levels of 10\u0000¹⁹\u0000, 10\u0000¹⁸\u0000, 10\u0000¹⁷\u0000 and 10\u0000¹⁶\u0000 atoms cm\u0000⁻³\u0000) in n-type GaN semiconductors. To precisely measure the reconstructed phase profiles in the GaN sample, three electron biprisms were used to obtain a series of high-contrast holograms without Fresnel fringes generated by a biprism filament, and a cryo-focused-ion-beam (cryo-FIB) was used to prepare a uniform TEM sample with less distortion in the wide field of view. All layers in a 350-nm-thick TEM sample were distinguished with 1.8-nm spatial resolution and 0.02-rad phase-resolution, and variations of step width in the phase profile (corresponding to depletion width) at the interfaces between the layers were also measured. Thicknesses of the active and inactive layers at each dopant level were estimated from the observed phase profile and the simulation of theoretical band structure. Ratio of active-layer thickness to total thickness of the TEM sample significantly decreased as dopant concentration decreased; thus, a thicker TEM sample is necessary to visualize lower carrier concentrations; for example, to distinguish layers with dopant concentrations of 10\u0000¹⁶\u0000 and 10\u0000¹⁵\u0000 atoms cm\u0000⁻³\u0000. It was estimated that sample thickness must be more than 700 nm to make it be possible to detect sub-layers by the combination of PS-EH and cryo-FIB. Phase-shifting electron holography precisely visualized layers with different concentrations of carriers activated by Si (at dopant levels of 10\u0000¹⁹\u0000, 10\u0000¹⁸\u0000, 10\u0000¹⁷\u0000, and 10\u0000¹⁶\u0000 atoms/cm\u0000³\u0000) in n-GaN semiconductors. A cryo-FIB and triple electron biprisms were used to prepare a uniform TEM sample and to acquire high-contrast holograms without Fresnel fringes.","PeriodicalId":18515,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/jmicro/dfz037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48172768","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":"Theory underpinning multislice simulations with plasmon energy losses","authors":"B G Mendis","doi":"10.1093/jmicro/dfaa003","DOIUrl":"10.1093/jmicro/dfaa003","url":null,"abstract":"The theoretical conditions for small-angle inelastic scattering where the incident electron can effectively be treated as a particle moving in a uniform potential is examined. The motivation for this work is the recent development of a multislice method that combines plasmon energy losses with elastic scattering using Monte Carlo methods. Since plasmon excitation is delocalized, it was assumed that the Bloch wave nature of the incident electron in the crystal does not affect the scattering cross-section. It is shown here that for a delocalized excitation the mixed dynamic form factor term of the scattering cross-section is zero and the scattered intensities follow a Poisson distribution. These features are characteristic of particle-like scattering and validate the use of Monte Carlo methods to model plasmon losses in multislice simulations.","PeriodicalId":18515,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/jmicro/dfaa003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37691856","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":"Lensless fourier transform electron holography applied to vortex beam analysis","authors":"Ken Harada;Yoshimasa A Ono;Yoshio Takahashi","doi":"10.1093/jmicro/dfaa008","DOIUrl":"10.1093/jmicro/dfaa008","url":null,"abstract":"Lensless Fourier transform holography has been developed. By treating Bragg diffraction waves as object waves and a transmitted spherical wave as a reference wave, these two waves are interfered and recorded as holograms away from the reciprocal plane. In this method, reconstruction of holograms requires only one Fourier transform. Application of this method to analyze vortex beams worked well and their amplitude and phase distributions were obtained on the reciprocal plane. By combining the conventional holography with the developed lensless Fourier transform holography, we can reconstruct and analyze electron waves from the real to reciprocal space continuously.","PeriodicalId":18515,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/jmicro/dfaa008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37771714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generative and discriminative model-based approaches to microscopic image restoration and segmentation","authors":"Shin Ishii;Sehyung Lee;Hidetoshi Urakubo;Hideaki Kume;Haruo Kasai","doi":"10.1093/jmicro/dfaa007","DOIUrl":"10.1093/jmicro/dfaa007","url":null,"abstract":"Image processing is one of the most important applications of recent machine learning (ML) technologies. Convolutional neural networks (CNNs), a popular deep learning-based ML architecture, have been developed for image processing applications. However, the application of ML to microscopic images is limited as microscopic images are often 3D/4D, that is, the image sizes can be very large, and the images may suffer from serious noise generated due to optics. In this review, three types of feature reconstruction applications to microscopic images are discussed, which fully utilize the recent advancements in ML technologies. First, multi-frame super-resolution is introduced, based on the formulation of statistical generative model-based techniques such as Bayesian inference. Second, data-driven image restoration is introduced, based on supervised discriminative model-based ML technique. In this application, CNNs are demonstrated to exhibit preferable restoration performance. Third, image segmentation based on data-driven CNNs is introduced. Image segmentation has become immensely popular in object segmentation based on electron microscopy (EM); therefore, we focus on EM image processing.","PeriodicalId":18515,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/jmicro/dfaa007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37774723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of focused ion-beam sampling for sidewall-roughness measurement of free-standing sub-μm objects by atomic force microscopy","authors":"Takaharu Nagatomi;Tatsuya Nakao;Yoko Fujimoto","doi":"10.1093/jmicro/dfz108","DOIUrl":"10.1093/jmicro/dfz108","url":null,"abstract":"In the present study, a free-standing object-sampling technique for microelectromechanical systems (MEMS) is developed to measure their sidewall surface roughnesses by atomic force microscopy (AFM). For this purpose, a conventional focused ion beam (FIB) sampling technique widely used for cross-sectional transmission electron microscope specimen preparation was applied. The sub-nm-order roughness parameters were quantitatively measured for sidewalls of Si-bridge test samples. The roughness parameters were compared before and after H\u0000<inf>2</inf>\u0000 annealing treatment, which induced smoothing of the surface by migration of the Si atoms. The reduction in the surface roughness by a factor of approximately one-third with 60-s H\u0000<inf>2</inf>\u0000 annealing was quantitatively evaluated by AFM. The present study confirms that the developed FIB–AFM technique is one potential approach for quantitatively evaluating the surface-roughness parameters on the oblique faces of free-standing objects in MEMS devices. FIB sampling technique was developed for AFM measurement of side-wall surface roughness of free-standing objects in MEMS devices. We confi rmed that the proposed FIB-AFM technique is one potential and practical approach to quantitatively evaluate surface roughness of oblique faces of free-standing objects in MEMS devices.","PeriodicalId":18515,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/jmicro/dfz108","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37547654","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":"Accuracy improvement of phase estimation in electron holography using noise reduction methods","authors":"Yoshihiro Midoh;Koji Nakamae","doi":"10.1093/jmicro/dfz115","DOIUrl":"10.1093/jmicro/dfz115","url":null,"abstract":"We try to improve the limit of the phase estimation of the interference fringe at low electron dose levels in electron holography by a noise reduction method. In this paper, we focus on unsupervised approaches to apply it to electron beam-sensitive and unknown samples and describe an overview of denoising methods used widely in image processing, such as wiener filter, total variation denoising, nonlocal mean filters and wavelet thresholding. We compare the wavelet hidden Markov model (WHMM) denoising that we have studied so far with the other conventional noise reduction methods. We evaluate the denoise performance of each method using the peak signal-to-noise ratio between noise-free and the target holograms (noisy or denoised holograms) and the root mean-square error (RMSE) between the true phase of the fringe and the measured phase by the discrete Fourier transform phase estimator. We show the denoised holograms for simulation and experimental data by using each noise reduction method and then discuss evaluation indexes obtained from these denoised holograms. From experimental results, it can be seen that the WHMM denoising can reduce the RMSE of fringe phase to about 1/4.5 for noisy simulation holograms and it has stable and good performance for noise reduction of observed holograms with various image qualities.","PeriodicalId":18515,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/jmicro/dfz115","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37576353","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":"Automated acquisition of vast numbers of electron holograms with atomic-scale phase information","authors":"Yoshio Takahashi;Tetsuya Akashi;Atsuko Sato;Toshiaki Tanigaki;Hiroyuki Shinada;Yasukazu Murakami","doi":"10.1093/jmicro/dfaa004","DOIUrl":"10.1093/jmicro/dfaa004","url":null,"abstract":"An automated acquisition system for collecting a large number of electron holograms, to improve the statistical precision of phase analysis, was developed. A technique for shifting the electron beam in combination with stage movement allows data to be acquired over a wide area of a TEM-specimen grid. Undesired drift in the hologram position, which may occur during the hologram acquisition, can be corrected in real time by automated detection of the interference-fringe region in an image. To demonstrate the usefulness of the developed automated hologram acquisition system, gold nanoparticles dispersed on a carbon foil were observed with a 1.2-MV atomic resolution holography electron microscope. The system could obtain 1024 holograms, which provided phase maps for more than 500 nanoparticles with a lateral resolution of 0.14 nm, in just 1 h. The observation results revealed an anomalous increase in mean inner potential for a particle size smaller than 4 nm. The developed automated hologram acquisition system can be applied to improve the precision of phase measurement by averaging many phase images, as demonstrated by single particle analysis for biological entities. Moreover, the system makes it possible to study electrostatic potential of catalysts and other functional nanoparticles at atomic resolution.","PeriodicalId":18515,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/jmicro/dfaa004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37692346","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":"Impaired actin dynamics and suppression of Shank2-mediated spine enlargement in cortactin knockout mice","authors":"Shinji Tanaka;Yasutaka Masuda;Akihiro Harada;Shigeo Okabe","doi":"10.1093/jmicro/dfaa001","DOIUrl":"10.1093/jmicro/dfaa001","url":null,"abstract":"Cortactin regulates actin polymerization and stabilizes branched actin network. In neurons, cortactin is enriched in dendritic spines that contain abundant actin polymers. To explore the function of cortactin in dendritic spines, we examined spine morphology and dynamics in cultured neurons taken from cortactin knockout (KO) mice. Histological analysis revealed that the density and morphology of dendritic spines were not significantly different between wild-type (WT) and cortactin KO neurons. Time-lapse imaging of hippocampal slice cultures showed that the extent of spine volume change was similar between WT and cortactin KO neurons. Despite little effect of cortactin deletion on spine morphology and dynamics, actin turnover in dendritic spines was accelerated in cortactin KO neurons. Furthermore, we detected a suppressive effect of cortactin KO on spine head size under the condition of excessive spine enlargement induced by overexpression of a prominent postsynaptic density protein Shank2. These results suggest that cortactin may have a role in maintaining actin organization by stabilizing actin filaments near the postsynaptic density. Cortactin is an actin-binding protein enriched in the synapse. Neurons without cortactin show accelerated spine actin turnover and reduced ability to increase spine size triggered by overexpression of Shank2, a prominent postsynaptic protein. Cortactin may play a role in actin fi lament maintenance and spine shape regulation in mammalian neurons.","PeriodicalId":18515,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/jmicro/dfaa001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37584530","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":"Energy-dispersive X-ray spectroscopy for an atomic-scale quantitative analysis of Pd–Pt core-shell nanoparticles","authors":"Shin Inamoto;Yuji Otsuka","doi":"10.1093/jmicro/dfz113","DOIUrl":"10.1093/jmicro/dfz113","url":null,"abstract":"The properties of core-shell nanoparticles, which are used for many catalytic processes as an alternative to platinum, depend on the size of both the particle and the shell. It is thus necessary to develop a quantitative method to determine the shell thickness. Pd–Pt core-shell particles were analyzed using scanning transmission electron microscopy (STEM) and energy-dispersive X-ray spectroscopy (EDX). Quantitative EDX line profiles acquired from the core-shell particle were compared to four core-shell models. The results indicate that the thickness of the Pt shell corresponds to two atomic layers. Meanwhile, high-angle annular dark-field STEM images from the same particle were analyzed and compared to simulated images. Again, this experiment demonstrates that the shell thickness was of two atomic layers. Our results indicate that, in small particles, it is possible to use EDX for a precise atomic-scale quantitative analysis. This article discusses the quantifi cation of EDX map acquired from Pd-Pt core-shell nanoparticles at the atomic scale. The EDX analysis provides that the thickness of the Pt shell corresponds to two atomic layers. The result indicates EDX is a great tool when studying core-shell nanoparticles.","PeriodicalId":18515,"journal":{"name":"Microscopy","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/jmicro/dfz113","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37576350","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}