Microscopy (Oxford, England)最新文献_第6页

Correction to: Structures of multisubunit membrane complexes with the CRYO ARM 200. 修正：多亚基膜复合物的结构与CRYO ARM 200。

Microscopy (Oxford, England) Pub Date : 2025-03-31 DOI: 10.1093/jmicro/dfae057

引用次数: 0

Improved dopant fraction variance estimation in statistical ALCHEMI based on correct error propagation rule. 基于正确的误差传播规则改进统计 ALCHEMI 中的掺杂分数方差估计。

Microscopy (Oxford, England) Pub Date : 2025-03-31 DOI: 10.1093/jmicro/dfae052

Akimitsu Ishizuka, Masahiro Ohtsuka, Shunsuke Muto

引用次数: 0

Cryo-STEM Tomography for Cell biology Using Thick Lamella. 利用厚薄片进行细胞生物学低温扫描电镜断层扫描。

Microscopy (Oxford, England) Pub Date : 2025-03-04 DOI: 10.1093/jmicro/dfaf017

Kazuhiro Aoyama, Hiroko Takazaki, Misaki Arie, Hironori Suemune, Shogo Kawai

引用次数: 0

Seg and Ref: A Newly Developed Toolset for Artificial Intelligence-Powered Segmentation and Interactive Refinement for Labor-Saving Three-Dimensional Reconstruction. Seg and Ref：新开发的人工智能分割和交互式细化工具集，用于省力的三维重建。

Microscopy (Oxford, England) Pub Date : 2025-03-03 DOI: 10.1093/jmicro/dfaf015

Satoru Muro, Takuya Ibara, Akimoto Nimura, Keiichi Akita

{"title":"Seg and Ref: A Newly Developed Toolset for Artificial Intelligence-Powered Segmentation and Interactive Refinement for Labor-Saving Three-Dimensional Reconstruction.","authors":"Satoru Muro, Takuya Ibara, Akimoto Nimura, Keiichi Akita","doi":"10.1093/jmicro/dfaf015","DOIUrl":"https://doi.org/10.1093/jmicro/dfaf015","url":null,"abstract":"Traditional three-dimensional reconstruction is labor-intensive owing to manual segmentation; this can be addressed by developing artificial intelligence-driven automated segmentation. However, it is limited by a lack of user-friendly tools for morphologists. We present a workflow for three-dimensional reconstruction using our artificial intelligence-powered segmentation tool. Specifically, we developed an interactive toolset, \"Seg & Ref,\" to overcome the abovementioned challenges by enabling artificial intelligence-powered segmentation and easy mask editing without requiring a command-line setup. We demonstrated a three-dimensional reconstruction workflow using serial sections of a Carnegie Stage 15 human embryo. Automated segmentation (Step 1) was performed using the graphical user interface, \"SAM2 GUI for Img Seq,\" which utilizes the Segment Anything Model 2 and supports interactive segmentation through a web-based interface. Users specify target structures via box prompts, and the results are propagated across all images for batch segmentation. The segmentation masks were reviewed and corrected (Step 2) using \"Segment Editor PP,\" a PowerPoint-based tool enabling interactive mask refinement. Finally, the corrected masks were imported into the 3D Slicer application for reconstruction (Step 3). Our three-dimensional reconstruction visualized key structures, including the spinal cord, veins, aorta, mesonephros, gut, heart, trachea, liver, and peritoneal cavity. The reconstructed models accurately represented their spatial relationships and morphologies. This provides a labor-saving approach for three-dimensional reconstruction workflows owing to their optimization for serial sections, versatility, and accessibility without programming expertise. Therefore, morphological research can be enhanced by precise segmentation using intuitive and user-friendly interfaces of \"Seg & Ref.\"","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tip treatment for subnanoscale atomic force microscopy in liquid by atomic layer deposition Al2O3 coating. 通过原子层沉积 Al2O3 涂层对液体中亚纳米尺度原子力显微镜的针尖进行处理。

Microscopy (Oxford, England) Pub Date : 2025-02-28 DOI: 10.1093/jmicro/dfaf014

Ryohei Kojima, Ayhan Yurtsever, Keisuke Miyazawa, Lucas J Andrew, Mark J MacLachlan, Takeshi Fukuma

{"title":"Tip treatment for subnanoscale atomic force microscopy in liquid by atomic layer deposition Al2O3 coating.","authors":"Ryohei Kojima, Ayhan Yurtsever, Keisuke Miyazawa, Lucas J Andrew, Mark J MacLachlan, Takeshi Fukuma","doi":"10.1093/jmicro/dfaf014","DOIUrl":"https://doi.org/10.1093/jmicro/dfaf014","url":null,"abstract":"Atomic force microscopy (AFM) allows direct imaging of atomic- or molecular-scale surface structures in liquid. However, such subnanoscale measurements are often sensitive to the AFM tip properties. To overcome this problem, 30 nm Si-sputter coating was proposed, and its effectiveness in improving stability and reproducibility has been demonstrated in atomic-scale imaging of various materials. However, this method involves tip blunting, enhancing the tip-induced dilation effect. As an alternative method, here we investigate atomic layer deposition (ALD) Al2O3-coating, where the film thickness is atomically well-controlled. Our transmission electron microscopy, contact angle and force curve measurements consistently suggest that as-purchased tips are covered with organic contaminants, and the initial 20 cycles gradually remove them, reducing the tip radius (Rt) and hydrophobicity. Further deposition increases Rt and hydrophilicity and forms an intact Al2O3 film over 50 cycles. We compared 50-cycle ALD-coated tips with 30 nm Si-sputter-coated tips in imaging mica and chitin nanocrystals (NCs). On mica, ALD coating gives slightly less stability and reproducibility in hydration force measurements than the Si sputter coating, yet they are sufficient in atomic-scale imaging. In imaging chitin NCs, ALD-coated tips give a less tip-induced dilation effect while maintaining molecular-scale imaging capability. We also found that 10-cycle-ALD coated tips covered with carbon give a better resolution and reproducibility in observing subnanoscale features at chitin NC surfaces. This result and our experience empirically suggest carbon-coated tips' effectiveness in observing carbon-based materials.","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Segmented ring-mesh model of glycosaminoglycan chains based on the 3D analysis of normal individual and Musculocontractural Ehlers-Danlos syndrome skin using scanning transmission electron microscopy. 基于扫描透射电镜对正常人和肌挛缩型埃勒-丹洛斯综合征皮肤三维分析的糖胺聚糖链分段环网模型

Microscopy (Oxford, England) Pub Date : 2025-02-18 DOI: 10.1093/jmicro/dfaf012

Naoki Takahashi, Takuya Hirose, Kiyokazu Kametani, Tomohito Iwasaki, Yasutada Imamura, Tomoki Kosho, Takafumi Watanabe

{"title":"Segmented ring-mesh model of glycosaminoglycan chains based on the 3D analysis of normal individual and Musculocontractural Ehlers-Danlos syndrome skin using scanning transmission electron microscopy.","authors":"Naoki Takahashi, Takuya Hirose, Kiyokazu Kametani, Tomohito Iwasaki, Yasutada Imamura, Tomoki Kosho, Takafumi Watanabe","doi":"10.1093/jmicro/dfaf012","DOIUrl":"https://doi.org/10.1093/jmicro/dfaf012","url":null,"abstract":"Collagen fibrils in the dermis are bundled by glycosaminoglycan (GAG) chains of decorin, which contribute to its strength. The three-dimensional structure of collagen fibrils and GAG chains has been discussed on the basis of observations and experiments. This study uses scanning transmission electron microscope (STEM) tomography with high Z-axis resolution to analyze the three-dimensional structure of GAG chains in the dermis from a healthy individual and a patient with Musculocontractural Ehlers-Danlos syndrome caused by pathogenic variants in CHST14 (mcEDS-CHST14). This observation revealed that the dermis from a healthy individual featured multiple GAG chains that wrapped around collagen fibrils and formed incomplete ring structures. However, in the dermis from a patient with mcEDS-CHST14, GAG chains were linear and did not form rings. Based on the relationship between collagen fibrils and GAG chains, we suggest the three-dimensional structure of normal GAG chains in a new model named the \"segmented ring-mesh model.\" The interactions between collagen fibrils and GAG chains in this model also apply to the dermis of mcEDS-CHST14 patients, in which the GAG chain composition changes to become CS-rich and more linear. This change leads to an increased inter-fibrillar space, which inhibits the dense packing of collagen fibrils. These findings suggest that this phenomenon contributes to the skin fragility observed in mcEDS-CHST14 patients. Our study suggests the \"segmented ring-mesh model\" of GAG chains is essential for the dense packing of collagen fibrils in normal dermis. STEM tomography is highly effective in analyzing the three-dimensional structure of collagen fibrils and GAG chains.","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Magnification calibration of X-ray 3D microscopy using micro-line structures. 利用微线结构校准 X 射线三维显微镜的放大倍率。

Microscopy (Oxford, England) Pub Date : 2025-01-30 DOI: 10.1093/jmicro/dfae045

Yasushi Azuma, Kazuhiro Kumagai, Naoki Kunishima, Koichiro Ito

{"title":"Magnification calibration of X-ray 3D microscopy using micro-line structures.","authors":"Yasushi Azuma, Kazuhiro Kumagai, Naoki Kunishima, Koichiro Ito","doi":"10.1093/jmicro/dfae045","DOIUrl":"10.1093/jmicro/dfae045","url":null,"abstract":"X-ray microscopy using computed tomography is an excellent 3D imaging instrument. Three-dimensional X-ray microscopy (3DXRM) is a nondestructive imaging technique used to inspect internal and external structures in units of submicrometers or less. The 3DXRM, although attractive, is mostly used as an observation instrument and is limited as a measurement system in quantitative evaluation and quality control. Calibration is required for use in measurement systems such as coordinate measurement systems, and specific standard samples and evaluation procedures are needed. The certified values of the standard samples must ideally be traceable to the International System of Units (SI). In the 3DXRM measurement system, line structures (LSs) are fabricated as prototype standard samples to conduct magnification calibration. In this study, we evaluated the LS intervals using calibrated cross-sectional scanning electron microscopy (SEM). A comparison of the evaluation results between SEM and 3DXRM for the LS intervals provided the magnification calibration factor for 3DXRM and validated the LSs, whereby the interval methods and feasibility of constructing an SI traceability system were evaluated using the calibrated SEM. Consequently, a magnification calibration factor of 1.01 was obtained for 3DXRM based on the intervals of the LSs evaluated by SEM. A possible route for realizing SI-traceable magnification calibration of 3DXRM has been presented.","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":"48-56"},"PeriodicalIF":0.0,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Precise measurement of spatial coherence and axial brightness based on the Wigner function reconstruction in transmission electron microscopes with field emission guns and a thermionic emission gun. 在配备场发射枪和热离子发射枪的透射电子显微镜中，根据维格纳函数重构精确测量空间相干性和轴向亮度。

Microscopy (Oxford, England) Pub Date : 2025-01-30 DOI: 10.1093/jmicro/dfae040

Shuhei Hatanaka, Jun Yamasaki

引用次数: 0

Simultaneous observation of multiple interferograms with Mach-Zehnder type electron interferometer on a 1.2-MV field-emission transmission electron microscope. 在 1.2-MV 场发射透射电子显微镜上使用马赫-泽恩德型电子干涉仪同时观测多个干涉图。

Microscopy (Oxford, England) Pub Date : 2025-01-30 DOI: 10.1093/jmicro/dfae030

Tetsuya Akashi, Yoshio Takahashi, Ken Harada

引用次数: 0

Total third-degree variation for noise reduction in atomic-resolution STEM images. 用于原子分辨率 STEM 图像降噪的总三度变异。

Microscopy (Oxford, England) Pub Date : 2025-01-30 DOI: 10.1093/jmicro/dfae031

Kazuaki Kawahara, Ryo Ishikawa, Shun Sasano, Naoya Shibata, Yuichi Ikuhara

{"title":"Total third-degree variation for noise reduction in atomic-resolution STEM images.","authors":"Kazuaki Kawahara, Ryo Ishikawa, Shun Sasano, Naoya Shibata, Yuichi Ikuhara","doi":"10.1093/jmicro/dfae031","DOIUrl":"10.1093/jmicro/dfae031","url":null,"abstract":"Scanning Transmission Electron Microscopy (STEM) enables direct determination of atomic arrangements in materials and devices. However, materials such as battery components are weak for electron beam irradiation, and low electron doses are required to prevent beam-induced damages. Noise removal is thus essential for precise structural analysis of electron-beam-sensitive materials at atomic resolution. Total square variation (TSV) regularization is an algorithm that exhibits high noise removal performance. However, the use of the TSV regularization term leads to significant image blurring and intensity reduction. To address these problems, we here propose a new approach adopting L2 norm regularization based on higher-order total variation. An atomic-resolution STEM image can be approximated as a set of smooth curves represented by quadratic functions. Since the third-degree derivative of any quadratic function is 0, total third-degree variation (TTDV) is suitable for a regularization term. The application of TTDV for denoising the atomic-resolution STEM image of CaF2 observed along the [001] zone axis is shown, where we can clearly see the Ca and F atomic columns without compromising image quality.","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141494463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0