Journal of microscopy最新文献_第2页

Analogue optical pattern recognition for cross-correlational CNN. 交叉相关CNN的模拟光学模式识别。

IF 1.9 4区工程技术

Journal of microscopy Pub Date : 2025-09-15 DOI: 10.1111/jmi.70034

Ahmed Farhat, Wim J C Melis

引用次数: 0

Leveraging modified ex situ tomography data for segmentation of in situ synchrotron X-ray computed tomography. 利用改进的非原位断层扫描数据进行原位同步加速器x射线计算机断层扫描的分割。

IF 1.9 4区工程技术

Journal of microscopy Pub Date : 2025-09-12 DOI: 10.1111/jmi.70032

Tristan Manchester, Adam Anders, Julio Spadotto, Hannah Eccleston, William Beavan, Hugues Arcis, Brian J Connolly

{"title":"Leveraging modified ex situ tomography data for segmentation of in situ synchrotron X-ray computed tomography.","authors":"Tristan Manchester, Adam Anders, Julio Spadotto, Hannah Eccleston, William Beavan, Hugues Arcis, Brian J Connolly","doi":"10.1111/jmi.70032","DOIUrl":"https://doi.org/10.1111/jmi.70032","url":null,"abstract":"In situ synchrotron X-ray computed tomography enables dynamic material studies. However, automated segmentation remains challenging due to complex imaging artefacts - like ring and cupping effects - and limited training data. We present a methodology for deep learning-based segmentation by transforming high-quality ex situ laboratory data to train models for segmentation of in situ synchrotron data, demonstrated through a metal oxide dissolution study. Using a modified SegFormer architecture, our approach achieves segmentation performance (94.7% IoU) that matches human inter-annotator reliability (94.6% IoU). This indicates the model has reached the practical upper bound for this task, while reducing processing time by 2 orders of magnitude per 3D dataset compared to manual segmentation. The method maintains robust performance over significant morphological changes during experiments, despite training only on static specimens. This methodology can be readily applied to diverse materials systems, enabling the efficient analysis of the large volumes of time-resolved tomographic data generated in typical in situ experiments across scientific disciplines.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145040426","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}

引用次数: 0

Crossing scales and eras: Correlative multimodal microscopy heritage studies. 跨越尺度和时代：相关的多模态显微镜遗产研究。

IF 1.9 4区工程技术

Journal of microscopy Pub Date : 2025-09-12 DOI: 10.1111/jmi.70030

Charles Wood, George Deakin, Atousa Moayedi, Jovana Radulovic

{"title":"Crossing scales and eras: Correlative multimodal microscopy heritage studies.","authors":"Charles Wood, George Deakin, Atousa Moayedi, Jovana Radulovic","doi":"10.1111/jmi.70030","DOIUrl":"https://doi.org/10.1111/jmi.70030","url":null,"abstract":"The comprehensive characterisation of complex, irreplaceable cultural heritage artefacts presents significant challenges for traditional analytical methods, which can fall short in providing multi-scale, non-invasive analysis. Correlative Multimodal Microscopy (CoMic), an approach that integrates data from multiple techniques, offers a powerful solution by bridging structural, chemical, and topographical information across different length scales. This paper provides a comprehensive review of the evolution, current applications, and future trajectory of CoMic within the field of heritage science. We present a historical overview of microscopy in heritage studies and detail the principles and advances of key techniques, such as electron, X-ray, optical, and probe microscopies. This review presents practical applications through case studies on materials that include wood, pigments, ceramics, metals, and textiles. To aid CoMic uptake, we also provide user-centric guides for researchers with diverse expertise. This review also examines the challenges that currently limit the widespread adoption of CoMic, challenges that include sample preparation, data correlation accuracy, high instrumental and resource costs, and the need for specialised interdisciplinary expertise. Although CoMic is a transformative methodology for artefact analysis and conservation, its full potential will be realised through future developments in accessible instrumentation, standardised protocols, and the integration of AI-driven data analysis. This review serves as a critical resource and roadmap for researchers, conservators, and institutions looking to harness the power of correlative microscopy to preserve our shared cultural legacy.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145040433","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}

引用次数: 0

Exploring collagen fibrillogenesis at the nanoscale: Tip-enhanced Raman imaging of protofibrils. 在纳米尺度上探索胶原纤维的形成：原纤维的尖端增强拉曼成像。

IF 1.9 4区工程技术

Journal of microscopy Pub Date : 2025-08-29 DOI: 10.1111/jmi.70029

Maria A Paularie, Emerson A Fonseca, Vitor Monken, André G Pereira, Rafael P Vieira, Ado Jorio

引用次数: 0

From cells to pixels: A decision tree for designing bioimage analysis pipelines. 从细胞到像素：设计生物图像分析管道的决策树。

IF 1.9 4区工程技术

Journal of microscopy Pub Date : 2025-08-29 DOI: 10.1111/jmi.70021

Elnaz Fazeli, Robert Haase, Michael Doube, Kota Miura, David Legland

引用次数: 0

Quantitative corrections for fluctuation electron microscopy. 波动电子显微镜的定量校正。

IF 1.9 4区工程技术

Journal of microscopy Pub Date : 2025-08-26 DOI: 10.1111/jmi.70027

J M Gibson, M M J Treacy

{"title":"Quantitative corrections for fluctuation electron microscopy.","authors":"J M Gibson, M M J Treacy","doi":"10.1111/jmi.70027","DOIUrl":"https://doi.org/10.1111/jmi.70027","url":null,"abstract":"Anomalously low values of the normalised variance in fluctuation electron microscopy (FEM) have been frequently reported. We present three experimental corrections for quantitative interpretation that significantly modify conventional approaches. FEM relies on measurements of intensity statistics in coherent nanodiffraction patterns. We demonstrate that sampling the nanodiffraction patterns with a pixelated detector removes high-frequency signals and reduces statistical variance. The most significant impact is on the background normalised variance, which arises from random atomic alignments and is distinct from the normalised variance peaks associated with the correlated alignments of medium-range order. Indeed, we show that if the peaks are background-subtracted, their height is much less affected by the detector effect, provided the experimental conditions are optimised. We show that shot noise correction must also be adjusted to account for the camera Modulation Transfer Function (MTF) effects. Additionally, we demonstrate through experiment that the traditional method of thickness correction for a-Si is inadequate and propose an alternative approach to address thickness variations. We speculate on the origin of the anomalous thickness effect in terms of displacement decoherence due to sample 'fluttering' under irradiation.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144957859","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}

引用次数: 0

Contrast by electron microscopy in thick biological specimens. 厚生物标本的电镜对比。

IF 1.9 4区工程技术

Journal of microscopy Pub Date : 2025-08-26 DOI: 10.1111/jmi.70026

Peter Rez, Lothar Houben, Shahar Seifer, Michael Elbaum

{"title":"Contrast by electron microscopy in thick biological specimens.","authors":"Peter Rez, Lothar Houben, Shahar Seifer, Michael Elbaum","doi":"10.1111/jmi.70026","DOIUrl":"https://doi.org/10.1111/jmi.70026","url":null,"abstract":"The contributions of coherent bright-field phase and incoherent dark-field amplitude contrast are investigated for thick biological specimens. A model for a T4 phage is constructed and images simulated for both TEM and STEM phase contrast using a multislice code. For TEM, the fraction of the illumination intensity available for phase contrast imaging is limited by the fraction of electrons in the zero loss peak, the plasmon peak, or the Landau distribution peak for very thick specimens. These were measured from electron energy loss spectra recorded from various thicknesses of vitreous ice. The incoherent amplitude contrast is simulated using the Penelope Monte Carlo code. Noise limits the features that can be distinguished under the low-dose conditions required for cryo-EM, even for high electron exposures of 100 electrons/Å2. Since in STEM post specimen optics are not used to form the image inelastically scattered electrons contribute to the recorded intensity. In principle STEM should have an advantage over TEM not just for incoherent amplitude contrast but also for coherent phase contrast beyond the limit of weak phase. The simulations suggest that it should be possible to image features in the phage embedded in 1 µm of vitreous ice when collection angles are optimised for bright or dark-field signals, with best contrast achieved for accelerating voltages of about 700 keV.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144957837","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}

引用次数: 0

Automatic identification and quantification of surface nanoscale pore morphology in coals of different ranks based on AFM, SEM and LP-N₂GA. 基于原子力显微镜（AFM）、扫描电镜（SEM）和LP-N2GA的不同等级煤表面纳米级孔隙形态自动识别与定量

IF 1.9 4区工程技术

Journal of microscopy Pub Date : 2025-08-26 DOI: 10.1111/jmi.70028

Dun Wu, Jianghao Wei, Shoule Zhao, Lin Sun, Yunfeng Li

{"title":"Automatic identification and quantification of surface nanoscale pore morphology in coals of different ranks based on AFM, SEM and LP-N2GA.","authors":"Dun Wu, Jianghao Wei, Shoule Zhao, Lin Sun, Yunfeng Li","doi":"10.1111/jmi.70028","DOIUrl":"https://doi.org/10.1111/jmi.70028","url":null,"abstract":"The pore structure characteristics of coal are crucial for coalbed methane adsorption and migration, carbon storage, and safety in deep coal mining. Although traditional methods can detect pore volume and distribution, they are limited in analysing pore morphology and surface properties. This study employs multiscale techniques including AFM (Atomic force microscopy), SEM (Scanning electron microscopy), and LP-N2GA (Low-Pressure nitrogen gas adsorption) to systematically analyse the impact of coal rank changes on pore structure and its evolutionary process, covering coals from medium-volatile to low-volatile bituminous and anthracite coals. AFM reveals the three-dimensional morphology and quantitative parameters of nanopores, SEM observes meso- and micropore structures, and LP-N2GA verifies pore size distribution. As coal rank increases, surface roughness decreases significantly, the number of pores increases, the average pore diameter decreases, pore morphology transforms from irregular to circular, and porosity increases. Specifically, as the rank of coal increases, the number of nanoring structures rises, while their diameters decrease. Changes in coal rank profoundly affect the nanoring structure, consistent with the evolutionary trend of surface morphology. The combination of AFM and LP-N2GA reveals the role of micropores in gas adsorption. This research not only provides a new perspective for understanding the influence of coal rank changes on pore structure characteristics but also offers a theoretical foundation for coalbed methane development, geological sequestration of carbon dioxide, design of coal-based functional materials, and coal mine safety prevention and control.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144957840","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}

引用次数: 0

Reconstruction of structured illumination microscopy for live imaging in low light with lightweight neural networks. 基于轻量级神经网络的结构照明显微镜微光成像重建。

IF 1.9 4区工程技术

Journal of microscopy Pub Date : 2025-08-22 DOI: 10.1111/jmi.70009

Hesong Jiang, Peihong Wu, Juan Zhang, Xueyuan Wang, Jinkun Zhan, Hexuan Tang

{"title":"Reconstruction of structured illumination microscopy for live imaging in low light with lightweight neural networks.","authors":"Hesong Jiang, Peihong Wu, Juan Zhang, Xueyuan Wang, Jinkun Zhan, Hexuan Tang","doi":"10.1111/jmi.70009","DOIUrl":"https://doi.org/10.1111/jmi.70009","url":null,"abstract":"Structured illumination microscopy (SIM) as a type of super-resolution optical microscopy technique has been widely used in the fields of biophysics, neuroscience, and cell biology research. However, this technique often requires high-intensity illumination and multiple image acquisitions to generate a single high-resolution image. This process not only significantly reduces the imaging speed, but also increases the exposure time of samples to intense light, leading to increased phototoxicity and photobleaching issues, especially prominent in live cell imaging. Here, we propose a lightweight Multi-Convolutional UNet (MCU-Net) aiming to maintain efficient super-resolution reconstruction performance by reducing the model parameter quantity. The algorithm integrates multiple convolutional techniques with multi-scale attention mechanisms, enhancing the model's sensitivity to information at different scales and improving its precise recognition ability for image textures and structures, thus enabling high-quality super-resolution reconstruction even under low-light conditions. The overall performance of the model is evaluated in terms of efficiency and accuracy, comparing MCU-Net with deep neural network models (UNet, ScUNet, EDSR, DFCAN) and traditional reconstruction algorithms (Wiener, HiFi, TV) across different cell types, lighting intensities, and various test sets. Experimental results show that compared to other deep learning models, MCU-Net achieves a 12.66% improvement in MS-SSIM and a 50.79% increase in NRMSE index. Its prediction accuracy remains stable even in the presence of low signal-to-noise ratio inputs. Furthermore, it strikes an optimal balance between reconstruction speed and model accuracy, with a 76.10% improvement in inference speed compared to the DFCAN model.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144957875","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}

引用次数: 0

Defocus correction and noise reduction using a hybrid ptychography and Centre-of-Mass algorithm 使用混合投影和质心算法进行离焦校正和降噪。

IF 1.9 4区工程技术

Journal of microscopy Pub Date : 2025-08-21 DOI: 10.1111/jmi.70010

Zhiyuan Ding, Chen Huang, Adrián Pedrazo-Tardajos, Angus I Kirkland, Peter D Nellist

{"title":"Defocus correction and noise reduction using a hybrid ptychography and Centre-of-Mass algorithm","authors":"Zhiyuan Ding, Chen Huang, Adrián Pedrazo-Tardajos, Angus I Kirkland, Peter D Nellist","doi":"10.1111/jmi.70010","DOIUrl":"10.1111/jmi.70010","url":null,"abstract":"Integrated Centre-of-Mass (iCOM) is a widely used phase-contrast imaging method based on Centre-of-Mass (COM), which makes use of a 4D Scanning Transmission Electron Microscopy (STEM) dataset using an in-focus probe. In this paper, we introduce a novel approach that combines Single-Side Band (SSB) ptychography with COM and iCOM, termed Side Band masked Centre-of-Mass (SBm-COM) and integrated Centre-of-Mass (SBm-iCOM) which is applicable to weak-phase objects. This method compensates for residual aberrations in 4DSTEM datasets while also reducing the noise contribution up to the <math>\u0000 <semantics>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 <mi>α</mi>\u0000 </mrow>\u0000 <annotation>$2alpha $</annotation>\u0000 </semantics></math> resolution limit. The aberration compensation and noise filtering features make the SBm-(i)COM suitable for samples that are difficult to focus or those that require minimal electron fluence. SBm-iCOM transfers the same information as SSB ptychography but results in an intrinsic transfer function that enhances low-frequency information.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"300 2","pages":"167-179"},"PeriodicalIF":1.9,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144957872","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}

引用次数: 0