Journal of microscopy最新文献

{"title":"Electrochemical scanning tunnelling microscopy: Concept, experiment, and application to organic layers on electrified surfaces.","authors":"Tomasz Kosmala, Bartosz Mądry, Paulina Wira, Anna Futyma, Serhii Kovalchuk, Ireneusz Morawski, Klaus Wandelt, Marek Nowicki","doi":"10.1111/jmi.13431","DOIUrl":"https://doi.org/10.1111/jmi.13431","url":null,"abstract":"<p><p>In this work, we present the concept and experimental possibilities of electrochemical scanning tunnelling microscopy (EC-STM). We describe the underlying physical principles of electron tunnelling microscopy and cyclic voltammetry, our design and construction of an integrated experimental set-up of both methods, as well as the operation of this home-built instrumentation. Exemplary results for bare and iodide and/or porphyrin-covered Cu(100), Cu(111), Au(100), and Au(111) surfaces, obtained with the use of this device, demonstrate the power of real-space imaging of solid surfaces 'in situ', that is, in solution, and 'in operando' with atomic resolution. The images are recorded in potentiostatic, potentiodynamic, and quasi spectroscopic modes of microscope operation, and enable the morphological and structural characterisation of crystalline electrode surfaces before and after adsorption of ions from solution as a function of the electrode potential. Here we present results of (i) the reconstructed and unreconstructed bare electrode surfaces, (ii) their surface modification caused by adsorbed iodide anions, and (iii) the self-assembly of co-adsorbed porphyrin molecules with characteristic ligands and empty cores. Detailed analyses of the high-resolution data yield complete sets of lattice parameters and transformation matrices, which correlate the structure of the respective porphyrin overlayer with the preadsorbed iodide as well as the crystalline substrate underneath. The systematic combination of 'in situ' STM and cyclic voltammetry (CV) data enables the elucidation of potential driven processes at the electrode surface, with or without charge transfer. These processes include the adsorption and desorption of atomic and molecular ions, the structural self-assembly and phase transitions of the atomic/molecular adsorbates as well as with-surface and on-surface reactions. In the present context, we place emphasis on 2D phase transitions within the adsorbed iodide layers and the self-assembly of the porphyrin molecules on the bare or iodide-covered surfaces recorded potentiostatically and potentiodynamically across a wide potential range. The potentiodynamic data are presented herein in the form of a movie. These model studies demonstrate the importance of combined 'in situ' STM and CV investigations - in short 'electrochemical scanning tunnelling microscopy (EC-STM)' - in the context of modern two-dimensional materials science. This includes the formation of functionalised surfaces, as well as electrocatalysis and electrosynthesis in a realistic aqueous environment. Lay description: The work concerns the concept and experimental possibilities of electrochemical scanning tunnelling microscopy (EC-STM) designed and built at the University of Bonn. The physical principles of electron tunnelling, cyclic voltammetry, and experimental set-up are presented. Exemplary results for bare, iodide, and porphyrin-covered copper and gold monocrystals are ","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144484687","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":"Fourier ptychography microscopy for digital pathology","authors":"Fraser Eadie,&nbsp;Laura Copeland,&nbsp;Giuseppe Di Caprio,&nbsp;Gail McConnell,&nbsp;Akhil Kallepalli","doi":"10.1111/jmi.70001","DOIUrl":"10.1111/jmi.70001","url":null,"abstract":"<p>Fourier ptychography microscopy (FPM) has made significant progress since its invention in 2013, thanks to its adaptable nature, high resolution, and vast field-of-view capabilities. FPM is used in various medical applications across multiple optical wavelengths, from automated digital pathology to radiology and ultraviolet label-free imaging. This review explores the fundamental physical and computational concepts that have driven advancements in digital pathology using FPM. A crucial part of the progress has been the development of computational algorithms, which have directly contributed to the improvements in FPM. We evaluate early-stage algorithms like the Gerchberg–Saxton and highlight how phase-retrieval and deep-learning advancements have propelled FPM forward. Additionally, we discuss the impact of these algorithms on digital pathology for potential automated diagnosis, providing a comprehensive explanation of their influence on medical imaging and offering insights into future research directions.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"300 2","pages":"260-285"},"PeriodicalIF":1.9,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144475668","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":"Background Remover – An effective tool for processing noisy microscopy images","authors":"A. Kilian,&nbsp;P. Bilski,&nbsp;M. Sankowska","doi":"10.1111/jmi.70002","DOIUrl":"10.1111/jmi.70002","url":null,"abstract":"<p><i>Background Remover</i> (<i>BGR</i>) is a novel software tool developed as a plugin to the well-known ImageJ program and designed to address the challenges of analysing fluorescent microscopy images characterised by low signal-to-noise ratios and heterogeneous backgrounds. The used algorithm effectively differentiates between signal and noise pixels, preserving the signal while eliminating noise. This functionality enables the analysis of images with objects of varying intensities, allowing for reliable identification even in low signal-to-noise ratio conditions. Furthermore, <i>BGR</i> offers the capability to determine the intensity of identified objects, enhancing its utility for researchers in the field. The paper describes the algorithm and the program functioning, as well as the carried out tests of its performance. The program is freely downloadable from the website https://kilianna.github.io/background-remover/</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"300 1","pages":"77-93"},"PeriodicalIF":1.9,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144475667","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":"Virtual dissection of Aedes aegypti mosquito using phase-contrast synchrotron microtomography","authors":"Gabriela Sena,&nbsp;Thaina Alvarenga,&nbsp;Ruan Ingliton Feio,&nbsp;Cícero Brasileiro Mello,&nbsp;Gabriel Fidalgo,&nbsp;Katrine Paiva,&nbsp;Tayane Tanure,&nbsp;Liebert Parreiras Nogueira,&nbsp;Marcos Vinícius Colaço,&nbsp;Arissa Pickler,&nbsp;Marcelo Salabert Gonzalez,&nbsp;Patricia Azambuja,&nbsp;Giuliana tromba,&nbsp;José Bento Pereira Lima,&nbsp;Ademir Xavier da Silva,&nbsp;Regina Cély Barroso","doi":"10.1111/jmi.70004","DOIUrl":"10.1111/jmi.70004","url":null,"abstract":"<p>In this paper, in-line phase-contrast synchrotron microtomography was used to study the morphology of adult <i>Aedes aegypti</i>. These specimens are vectors of several arboviruses, causing dengue, chikungunya, Zika and yellow fever. The morphological details of this insect species are still incomplete and insufficient. To address this gap, this study examined whole specimens of <i>Aedes aegypti</i> in the adult phase at high resolution. For this, the adult samples were scanned in the microtomography beamline (SYRMEP) at the Italian Synchrotron Light Laboratory (ELETTRA). The phase-contrast technique allowed us to obtain high-quality images, which made it possible to evaluate the segmentation of structures on the rendered volume by the Dragonfly software. The combination of high-quality images and segmentation process provide adequate visualisation of different organs which could serve in assessing the effectiveness of innovative control population methods as a basis for future control studies of the insect vector.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"300 1","pages":"68-76"},"PeriodicalIF":1.9,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144475669","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":"TOC - Issue Information","authors":"","doi":"10.1111/jmi.13328","DOIUrl":"https://doi.org/10.1111/jmi.13328","url":null,"abstract":"","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"299 1","pages":"1-2"},"PeriodicalIF":1.5,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13328","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281600","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":"Artificial intelligence-powered microscopy: Transforming the landscape of parasitology.","authors":"Mariana De Niz, Sara Silva Pereira, David Kirchenbuechler, Leandro Lemgruber, Constadina Arvanitis","doi":"10.1111/jmi.13433","DOIUrl":"https://doi.org/10.1111/jmi.13433","url":null,"abstract":"<p><p>Microscopy and image analysis play a vital role in parasitology research; they are critical for identifying parasitic organisms and elucidating their complex life cycles. Despite major advancements in imaging and analysis, several challenges remain. These include the integration of interdisciplinary data; information derived from various model organisms; and data acquired from clinical research. In our view, artificial intelligence-with the latest advances in machine and deep learning-holds enormous potential to address many of these challenges. This review addresses how artificial intelligence, machine learning and deep learning have been used in the field of parasitology-mainly focused on Apicomplexan, Diplomonad, and Kinetoplastid groups. We explore how gaps in our understanding could be filled by AI in future parasitology research and diagnosis in the field. Moreover, it addresses challenges and limitations currently faced in implementing and expanding the use of artificial intelligence across biomedical fields. The necessary increased collaboration between biologists and computational scientists will facilitate understanding, development, and implementation of the latest advances for both scientific discovery and clinical impact. Current and future AI tools hold the potential to revolutionise parasitology and expand One Health principles.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258281","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":"Comparative morphological characterisation of SARS-CoV-2 and influenza B virus using atomic force microscopy","authors":"Junru Wang,&nbsp;Nan Li,&nbsp;Yujuan Chen,&nbsp;Jingyu Wang,&nbsp;Junxi Wang,&nbsp;Chunyang Gao,&nbsp;Jing Hu,&nbsp;Zuobin Wang","doi":"10.1111/jmi.13432","DOIUrl":"10.1111/jmi.13432","url":null,"abstract":"<p>Influenza B virus and SARS-CoV-2 virus are the two most representative respiratory infectious diseases. These two viruses not only show similarities in clinical symptoms but also have numerous similarities in microstructure, which is difficult to distinguish and poses great challenges for diagnosis. In this work, the three-dimensional structures and surface features of influenza B virus and SARS-CoV-2 virus were investigated using atomic force microscopy. The results indicated that there were substantial differences in surface morphology and structure between the two viruses. Specifically, the average diameter of SARS-CoV-2 virus particles was around 222.8 nm while that of influenza B virus particles is smaller at about 191.2 nm. The height of SARS-CoV-2 particles was also larger, averaging about 30–60 nm, while that of influenza B virus particles averaged around 10–30 nm. Additionally, the crown-like structure on the surface of the SARS-CoV-2 virus was sparser and more prominent than that of the influenza virus. These findings offer significant insights into the distinction between the two viruses, aiding in the accurate characterisation of SARS-CoV-2 and influenza viruses and facilitating timely and effective treatment strategies.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"300 1","pages":"27-35"},"PeriodicalIF":1.9,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127940","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":"Facile electrochemical synthesis of binder-free tin nanostructures on carbon foam: A promising electrode for high-efficiency supercapacitors","authors":"Muhammad Zainul Abadin,&nbsp;Ahtisham Abdul Wahid,&nbsp;Muhammad Usman","doi":"10.1111/jmi.13427","DOIUrl":"10.1111/jmi.13427","url":null,"abstract":"<p>Energy storage technologies that are efficient are in constant demand. Supercapacitors have attracted much interest among these gadgets because of their superior cycle stability and high-power density. This work used a simple and cost-effective sonication-assisted electrodeposition approach to develop tin oxide nanoparticles on functionalised carbon foam substrate with different concentration ratios (1 mM, 3 mM, and 5 mM). FTIR, XRD, and SEM validated the chemical, structural, and morphological characteristics of all nanostructured electrodes. The tetragonal structure with spherical shape was the result of the fine crystallisation of the tin oxide nanoparticles. The electrochemical characteristics are evaluated by CV, EIS, and GCD testing. Among all electrodes, Sn₁@CF has a larger electrochemically active surface area, low internal resistance, and high specific capacitance. These findings underscore that the binder-free Sn₁@CF electrode is a promising candidate for high-efficiency supercapacitor applications.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"300 1","pages":"18-26"},"PeriodicalIF":1.9,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094017","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":"Simple Python-based methods for analysis and drift-correction of STM images.","authors":"Francesco Cazzadori, Alessandro Facchin, Silvio Reginato, Christian Durante","doi":"10.1111/jmi.13426","DOIUrl":"https://doi.org/10.1111/jmi.13426","url":null,"abstract":"<p><p>A successful scanning tunnelling microscopy (STM) experiment relies on both delicate sample preparation and measurement, and careful image filtering and analysis to provide clear and solid results. Processing and analysis of STM images may result in a tricky task, due to the complexity and specificity of the probed systems. In this paper, we introduce our recently developed, simple Python-based methods for filtering and analysing STM images, with the aim of providing a semi-quantitative treatment of the input data. Case studies will be presented using images obtained through electrochemical STM. Additionally, we propose a straightforward yet effective universal drift-correction tool for SPM image sequences.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144017940","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":"PerfectlyAverage: A classical open-source software method to determine the optimal averaging parameters in laser scanning fluorescence microscopy","authors":"S. Foylan,&nbsp;L. M. Rooney,&nbsp;W. B. Amos,&nbsp;G. W. Gould,&nbsp;G. McConnell","doi":"10.1111/jmi.13425","DOIUrl":"10.1111/jmi.13425","url":null,"abstract":"<p>Laser scanning fluorescence microscopy (LSFM) is a widely used imaging method, but image quality is often degraded by noise. Averaging techniques can enhance the signal-to-noise ratio (SNR), but while this can improve image quality, excessive frame accumulation can introduce photobleaching and may lead to unnecessarily long acquisition times. A classical software method called PerfectlyAverage is presented to determine the optimal number of frames for averaging in LSFM using SNR, photobleaching, and power spectral density (PSD) measurements. By assessing temporal intensity variations across frames in a time series, PerfectlyAverage identifies the point where additional averaging ceases to provide significant noise reduction. Experiments with fluorescently stained tissue paper and fibroblast cells validated the approach, demonstrating that up to a fourfold reduction in averaging time may be possible. PerfectlyAverage is open source, compatible with any LSFM data, and it is aimed at improving imaging workflows while reducing the reliance on subjective criteria for choosing the number of averages.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"299 2","pages":"155-165"},"PeriodicalIF":1.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13425","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144007266","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}