Ultramicroscopy最新文献_第7页

Prediction of the morphology of nano particles based solely on atom counting data 仅基于原子计数数据的纳米粒子形态预测

IF 2.1 3区工程技术

Ultramicroscopy Pub Date : 2025-05-02 DOI: 10.1016/j.ultramic.2025.114139

Ivo Alxneit

{"title":"Prediction of the morphology of nano particles based solely on atom counting data","authors":"Ivo Alxneit","doi":"10.1016/j.ultramic.2025.114139","DOIUrl":"10.1016/j.ultramic.2025.114139","url":null,"abstract":"<div><div>The framework to determine the morphology of nano particles from atomically resolved electron microscopy images and atom counting data is introduced. Focus is placed on electron microscopy data avoiding advanced geometry optimization of the particle. The problem is solved by simulated annealing with different fitness functions assessed. Even for small particles the solution space rapidly becomes too large to be exhausted. The concept of site occupation probabilities, <span><math><msub><mrow><mi>p</mi></mrow><mrow><mi>i</mi></mrow></msub></math></span>, is then used to analyze a subset, typically very few hundred solutions. This is shown to be sufficient to reach a relative error of below 10% for <span><math><mrow><msub><mrow><mi>p</mi></mrow><mrow><mi>i</mi></mrow></msub><mo>></mo><mn>0</mn><mo>.</mo><mn>5</mn></mrow></math></span> already with 100 solutions allowing to determine with high confidence and low statistical error realistic average shapes also for nano particles of a few thousand atoms. These particles typically exhibit a well defined core covered by a layer of sites that are not occupied in each solution. It is further demonstrated that sites with high probability to contain a vacancy can be identified <em>assuming</em> the presence of a vacancy. If a vacancy is actually present in a particle its position can be identified with rather high fidelity. Finally, it is shown that the procedure can cope with the statistical error or ambiguities inherent in atom counting data based on noisy, low dose electron microscopy images.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"275 ","pages":"Article 114139"},"PeriodicalIF":2.1,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144123527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Robust projection parameter calibration in cryo-ET with L1-norm optimization 基于l1范数优化的cryo-ET鲁棒投影参数标定

IF 2.1 3区工程技术

Ultramicroscopy Pub Date : 2025-04-29 DOI: 10.1016/j.ultramic.2025.114134

Shengkai Guo , Zihe Xu , Xinyan Li , Zhidong Yang , Chenjie Feng , Renmin Han

{"title":"Robust projection parameter calibration in cryo-ET with L1-norm optimization","authors":"Shengkai Guo , Zihe Xu , Xinyan Li , Zhidong Yang , Chenjie Feng , Renmin Han","doi":"10.1016/j.ultramic.2025.114134","DOIUrl":"10.1016/j.ultramic.2025.114134","url":null,"abstract":"<div><div>Fiducial marker-based alignment in cryo-electron tomography (cryo-ET) has been extensively studied over a long period. The calibration of projection parameters using nonlinear least squares technique methodologies stands as the ultimate and pivotal stage in the alignment procedure. The efficacy of calibration is substantially impacted by noise and outliers in the marker data obtained from previous steps. Several robust fitting methods have been explored and implemented to address this issue by improving marker data or assigning weights to markers. However, these methods have their own limitations and often assume general Gaussian noise assumption, which may not accurately represent the distribution of noise and outliers in the marker data. In this work, we propose a robust projection parameter calibration model based on <span><math><msub><mrow><mi>L</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span>-norm optimization under Laplace noise assumption in order to overcome the limitations of existing methods. To efficiently solve the problem, we also design a faster and stabler first-order non-sparse method based on smooth approximation strategy. Additionally, we introduce subgradient and subdifferential for mathematical analysis. The accuracy, robustness, and efficacy of our approach are demonstrated through both simulated and real-world experiments.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"274 ","pages":"Article 114134"},"PeriodicalIF":2.1,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143907639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

On the impulse approximation in electron Compton scattering 电子康普顿散射中的脉冲近似

IF 2.1 3区工程技术

Ultramicroscopy Pub Date : 2025-04-26 DOI: 10.1016/j.ultramic.2025.114153

BG Mendis

引用次数: 0

Opportunities and challenges to determine surface free energy of chocolates on microscopic scale from atomic force microscopy adhesion measurements 原子力显微镜黏附测量在微观尺度上测定巧克力表面自由能的机遇与挑战

IF 2.1 3区工程技术

Ultramicroscopy Pub Date : 2025-04-18 DOI: 10.1016/j.ultramic.2025.114150

Sarah Schroeder , Koen Dewettinck , Volker Heinz , Ute Bindrich , Dana Middendorf , Knut Franke

{"title":"Opportunities and challenges to determine surface free energy of chocolates on microscopic scale from atomic force microscopy adhesion measurements","authors":"Sarah Schroeder , Koen Dewettinck , Volker Heinz , Ute Bindrich , Dana Middendorf , Knut Franke","doi":"10.1016/j.ultramic.2025.114150","DOIUrl":"10.1016/j.ultramic.2025.114150","url":null,"abstract":"<div><div>Surface free energy (SFE) is an important surface property in food processing as it determines the wettability of solid surfaces or the interaction of mould surfaces and chocolate during the moulding process. High-resolution information about SFE could be useful to understand gloss inhomogeneities of chocolates after de-moulding. SFE is connected with adhesion properties. Thus, Atomic force microscopy (AFM) adhesion measurements can be applied to determine SFE of a solid surface at microscopic scale. For this purpose, AFM tips were functionalized to modify their SFE and used for adhesion measurements at three different chocolate gloss areas (matt, glossy and homogenous) via AFM force maps. Influence of relevant parameters such as surface roughness, contact area, relative humidity, and SFE of functionalized tips was considered. Two different mathematical approaches based on Johnson-Kendall-Roberts theory were used to calculate SFE from adhesion values. The measured adhesion values showed variations depending on functionalized tip and chocolate gloss area. The results showed a difference in adhesion and, consequently, SFE in the different gloss areas with gloss > homogenous > matt. However, SFE obtained from adhesion forces were not decisive enough to enable a direct correlation with SFE data from contact angle measurements at the same area.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"273 ","pages":"Article 114150"},"PeriodicalIF":2.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143855695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Influence of experimental conditions on apparent AFM tip-surface contact in air 空气中实验条件对AFM尖端表面表观接触的影响

IF 2.1 3区工程技术

Ultramicroscopy Pub Date : 2025-04-18 DOI: 10.1016/j.ultramic.2025.114148

Ilya A. Morozov, Roman I. Izyumov

{"title":"Influence of experimental conditions on apparent AFM tip-surface contact in air","authors":"Ilya A. Morozov, Roman I. Izyumov","doi":"10.1016/j.ultramic.2025.114148","DOIUrl":"10.1016/j.ultramic.2025.114148","url":null,"abstract":"<div><div>Accurate determination of the onset of the contact between the atomic force microscope (AFM) tip and the surface in force measurements is necessary both for calculating the constants of non-contact interactions and for determining the structural and mechanical properties of the materials. In an air environment the contact is preceded by a rapid jump of the tip to the surface due to attractive forces. If a surface is not deformed by a probe of a given stiffness, the end of the jump (minimum of the deflection of the cantilever) is taken as the onset of the contact. In this work, it is shown that the tip contacts with the deformable surface before the completion of the jump. It is reasonable to use the point of the extreme deflection velocity as the onset of the contact. A dynamic mass-spring model of the interaction of the tip with the viscoelastic material has shown that the high deflection velocity and the low rate of data acquisition (bandwidth) are the reasons for significant errors in determining the contact from the experimental force curve. In the most cases, the observed contact point is lower than the actual one (under certain conditions, the opposite situation is also possible) and the measurement error is at least 50 % (depending on the experimental settings, the properties of the probe and the material).</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"273 ","pages":"Article 114148"},"PeriodicalIF":2.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143870563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Capacitance compensation on a double-barrel nanopipette for improving current detection of scanning ion conductance microscopy 双管纳米吸管的电容补偿提高扫描离子电导显微镜的电流检测

IF 2.1 3区工程技术

Ultramicroscopy Pub Date : 2025-04-18 DOI: 10.1016/j.ultramic.2025.114149

Futoshi Iwata , Naoto Fukuzawa , Hitoshi Inomata , Kenta Nakazawa , Toshi Nagata , Hideya Kawasaki , Osamu Hoshi

{"title":"Capacitance compensation on a double-barrel nanopipette for improving current detection of scanning ion conductance microscopy","authors":"Futoshi Iwata , Naoto Fukuzawa , Hitoshi Inomata , Kenta Nakazawa , Toshi Nagata , Hideya Kawasaki , Osamu Hoshi","doi":"10.1016/j.ultramic.2025.114149","DOIUrl":"10.1016/j.ultramic.2025.114149","url":null,"abstract":"<div><div>We developed a method to improve the current-detection response of scanning ion conduction microscopy (SICM) using a double-barrel nanopipette. By detecting the difference between the two signals from each channel, capacitive currents can be canceled out, resulting in an improved ion current detection response and reduced imaging time in bias-modulated scanning ion conductance microscopy operated with AC bias voltages (BM-SICM). Furthermore, this method can reduce the synchronized capacitive current noise of two adjacent channels of a double-barrel nanopipette by canceling each other via a differential operation. Therefore, an improved detection signal was achieved even in the SICM operated with a DC bias voltage by reducing the noise from the piezoelectric scanner. As demonstrated by the proposed method, chromosomes that were difficult to observe owing to their strong negative charges were clearly imaged in the BM-SICM operated with an AC bias voltage without artifacts caused by surface charging. Additionally, in SICM operating with a DC bias voltage, dynamic interaction among an intracellular short rod, <em>Listeria monocytogenes</em>, and Caco-2 human enterocyte-like cells was successfully observed.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"273 ","pages":"Article 114149"},"PeriodicalIF":2.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143864533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A novel method for through-silicon via characterization based on diffraction fringe analysis 基于衍射条纹分析的硅通孔表征新方法

IF 2.1 3区工程技术

Ultramicroscopy Pub Date : 2025-04-08 DOI: 10.1016/j.ultramic.2025.114136

Pengfei Lin, Kuan Lu, ChaBum Lee

引用次数: 0

Emittance minimization for aberration correction I: Aberration correction of an electron microscope without knowing the aberration coefficients 用于像差校正的发射率最小化 I：在不知道像差系数的情况下校正电子显微镜的像差

IF 2.1 3区工程技术

Ultramicroscopy Pub Date : 2025-04-05 DOI: 10.1016/j.ultramic.2025.114137

Desheng Ma , Steven E. Zeltmann , Chenyu Zhang , Zhaslan Baraissov , Yu-Tsun Shao , Cameron Duncan , Jared Maxson , Auralee Edelen , David A. Muller

{"title":"Emittance minimization for aberration correction I: Aberration correction of an electron microscope without knowing the aberration coefficients","authors":"Desheng Ma , Steven E. Zeltmann , Chenyu Zhang , Zhaslan Baraissov , Yu-Tsun Shao , Cameron Duncan , Jared Maxson , Auralee Edelen , David A. Muller","doi":"10.1016/j.ultramic.2025.114137","DOIUrl":"10.1016/j.ultramic.2025.114137","url":null,"abstract":"<div><div>Precise alignment of the electron beam is critical for successful application of scanning transmission electron microscopes (STEM) to understanding materials at atomic level. Despite the success of aberration correctors, aberration correction is still a complex process. Here we approach aberration correction from the perspective of accelerator physics and show it is equivalent to minimizing the emittance growth of the beam, the span of the phase space distribution of the probe. We train a deep learning model to predict emittance growth from experimentally accessible Ronchigrams. Both simulation and experimental results show the model can capture the emittance variation with aberration coefficients accurately. We further demonstrate the model can act as a fast-executing function for the global optimization of the lens parameters. Our approach enables new ways to quickly quantify and automate aberration correction that takes advantage of the rapid measurements possible with high-speed electron cameras. In part II of the paper, we demonstrate how the emittance metric enables rapid online tuning of the aberration corrector using Bayesian optimization.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"273 ","pages":"Article 114137"},"PeriodicalIF":2.1,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143821413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Emittance Minimization for Aberration Correction II: Physics-informed Bayesian Optimization of an Electron Microscope 发射最小的像差校正II：一个电子显微镜的物理通知贝叶斯优化

IF 2.1 3区工程技术

Ultramicroscopy Pub Date : 2025-04-04 DOI: 10.1016/j.ultramic.2025.114138

Desheng Ma , Steven E. Zeltmann , Chenyu Zhang , Zhaslan Baraissov , Yu-Tsun Shao , Cameron Duncan , Jared Maxson , Auralee Edelen , David A. Muller

{"title":"Emittance Minimization for Aberration Correction II: Physics-informed Bayesian Optimization of an Electron Microscope","authors":"Desheng Ma , Steven E. Zeltmann , Chenyu Zhang , Zhaslan Baraissov , Yu-Tsun Shao , Cameron Duncan , Jared Maxson , Auralee Edelen , David A. Muller","doi":"10.1016/j.ultramic.2025.114138","DOIUrl":"10.1016/j.ultramic.2025.114138","url":null,"abstract":"<div><div>Aberration-corrected Scanning Transmission Electron Microscopy (STEM) has become an essential tool in understanding materials at the atomic scale. However, tuning the aberration corrector to produce a sub-Ångström probe is a complex and time-costly procedure, largely due to the difficulty of precisely measuring the optical state of the system. When measurements are both costly and noisy, Bayesian methods provide rapid and efficient optimization. To this end, we develop a Bayesian approach to fully automate the process by minimizing a new quality metric, beam emittance, which is shown to be equivalent to performing aberration correction. In part I, we derived several important properties of the beam emittance metric and trained a deep neural network to predict beam emittance growth from a single Ronchigram. Here we use this as the black box function for Bayesian Optimization and demonstrate automated tuning of simulated and real electron microscopes. We explore different surrogate functions for the Bayesian optimizer and implement a deep neural network kernel to effectively learn the interactions between different control channels without the need to explicitly measure a full set of aberration coefficients. Both simulation and experimental results show the proposed method outperforms conventional approaches by achieving a better optical state with a higher convergence rate.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"273 ","pages":"Article 114138"},"PeriodicalIF":2.1,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143821412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Splicing dual-range EELS spectra: Identifying and correcting artefacts 拼接双量程EELS光谱：识别和校正伪影

IF 2.1 3区工程技术

Ultramicroscopy Pub Date : 2025-04-01 DOI: 10.1016/j.ultramic.2025.114135

Alan J. Craven , Bianca Sala , Donald A. MacLaren , Sam McFadzean , Bernhard Schaffer , Ian MacLaren

{"title":"Splicing dual-range EELS spectra: Identifying and correcting artefacts","authors":"Alan J. Craven , Bianca Sala , Donald A. MacLaren , Sam McFadzean , Bernhard Schaffer , Ian MacLaren","doi":"10.1016/j.ultramic.2025.114135","DOIUrl":"10.1016/j.ultramic.2025.114135","url":null,"abstract":"<div><div>In dual or multiple range electron energy loss spectroscopy, splicing the low loss spectra together with core loss ranges allows Fourier-log deconvolution of the entire energy range. However, because of the huge intrinsic dynamic range in EELS, the intensity at the splice point in a low loss spectrum is typically small, meaning that even weak or subtle artefacts can have big effects. Three main sources of artefacts in a Gatan GIF Quantum system have been investigated: non-uniformity of energy dispersion caused by aberrations in the spectrometer optics, stray scattering in the detector chamber, and small differences between the responsivity of the different detector quadrants. We present methods to measure, quantify and correct these artefacts. Ideally, the ratio for scaling at the splice should be the ratio of integration times. Prior to correction, the scaling factor is found to be about 15 % less than the exposure or time ratio and is dependent on the specimen thickness. After correction, the discrepancies are less than 0.5 %. This allows quantitative comparison of data taken at different points in time, even after major system changes, provided suitable artefact-correction datasets are taken. Whilst the detail is specific to one particular instrument, the principles are also applicable to newer spectrometers, including those with direct electron detectors.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"272 ","pages":"Article 114135"},"PeriodicalIF":2.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143785528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0