Journal of microscopy最新文献

{"title":"Commentary on critique and rebuttal of ‘On the pixel selection criterion for the calculation of the Pearson's correlation coefficient in fluorescence microscopy’","authors":"Fabrice Cordelieres, Michelle Peckham","doi":"10.1111/jmi.70006","DOIUrl":"10.1111/jmi.70006","url":null,"abstract":"","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"299 2","pages":"91-93"},"PeriodicalIF":1.5,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144591471","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":"Response to Adler and Parmryd","authors":"Sergio G. Lopez,&nbsp;Sebastian Samwald,&nbsp;Sally Jones,&nbsp;Christine Faulkner","doi":"10.1111/jmi.13428","DOIUrl":"10.1111/jmi.13428","url":null,"abstract":"<p>The Pearson Correlation Coefficient can be calculated using three different criteria for pixel selection. These criteria carry different implications for interpretation of the metric. Different image analysis tools use these different criteria, and it is important that users know which criteria they have used. We maintain that this is important information for the community to consider and that we accurately addressed this topic. Adler and Parmryd have identified a flaw in our analysis in Figure 2 and here we explain how this came about and provide a correction. Alder and Parmryd's letter maligns our intent and competency – we refute all accusations and we object to the use of <i>ad hominem</i> arguments in scientific discourse.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"299 2","pages":"99-103"},"PeriodicalIF":1.5,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144591474","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":"Optimisation of freeze substitution protocols for the examination of malaria parasite structure by volumetric electron microscopy.","authors":"Rachel Rachid, Camila Wendt, Wanderley de Souza, Kildare Miranda","doi":"10.1111/jmi.70007","DOIUrl":"https://doi.org/10.1111/jmi.70007","url":null,"abstract":"<p><p>Malaria is one of the deadliest infectious diseases in the world, annually responsible for over 400,000 deaths. It is caused by parasites of the genus Plasmodium, which undergo remarkable structural changes during their development within different cells across various hosts. An important approach to understand the structural basis of biochemical and physiological processes during Plasmodium infection has been the quantitative measurement of dimensional parameters obtained by different microscopy techniques. In this regard, sample preparation, particularly electron microscopy protocols that rely on room-temperature chemical fixation, has posed significant challenges, as it is known to produce artefacts such as shrinking, swelling and displacement of structures and osmolytes. In contrast, specimen immobilisation by cryofixation followed by freeze substitution minimises these artefacts and provides better sample preservation. Nevertheless, the composition of the freeze substitution medium may vary depending on the cell type, making it a critical factor for achieving optimal sample preparation. In this work, we optimised a freeze substitution protocol for the structural analysis of intraerythrocytic stages of the murine malaria models Plasmodium chabaudi and P. berghei. We tested different freeze substitution recipes, considering the biochemical composition of malaria membranes, and compared the results with those obtained through conventional chemical fixation. Overall, the results showed a significant improvement on the preservation of cell morphology and haemozoin crystals. Establishing an efficient and reproducible freeze substitution protocol for murine malaria models provides an important tool for advancing our understanding of the structural organisation of Plasmodium spp.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144591472","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":"Quantifying colocalisation by correlation: Use pixels with both fluorophores within biologically meaningful ROIs","authors":"Jeremy Adler,&nbsp;Ingela Parmryd","doi":"10.1111/jmi.13429","DOIUrl":"10.1111/jmi.13429","url":null,"abstract":"","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"299 2","pages":"94-98"},"PeriodicalIF":1.5,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144591473","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":"A workflow for semi-automated volume correlative light microscopy and transmission electron tomography.","authors":"Kohki Konishi, Guilherme Neves, Matthew Russell, Masafumi Mimura, Juan Burrone, Roland Fleck","doi":"10.1111/jmi.13436","DOIUrl":"https://doi.org/10.1111/jmi.13436","url":null,"abstract":"<p><p>Volume Correlative Light and Electron Microscopy (vCLEM) is a powerful method for assessing the ultrastructure of molecularly defined subcellular domains. A central challenge in vCLEM has been the efficient navigation of Regions of Interest (ROIs) across multimodal and multiscale imaging datasets. We developed two key tools to overcome this challenge. First, we developed a multimodal image registration tool (SegReg) that utilizes segmentation of common objects across modalities and uses a Graphical Processing Unit (GPU) for registration of imaging datasets in two and three dimensions. Secondly, we developed a dedicated image viewer to visualize multimodal image registration in three dimensions (NavROI). Here, we demonstrate the integrated use of SegReg and NavROI to navigate large mouse tissue blocks with preserved fluorescent signals to allow selective targeting for TEM tomography of ROIs containing synapses and the cisternal organelle on the proximal region of the axon of a selected pyramidal neuron. By providing real time guidance to precise X-Y trimming of selected ROIs, reliable estimates of cutting depth relative to ROIs and a clear visual navigation of multimodal and multiscale images, our integrated workflow significantly improves the efficiency and accessibility of vCLEM analysis.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144528416","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":"DeepEM Playground: Bringing deep learning to electron microscopy labs.","authors":"Hannah Kniesel, Poonam Poonam, Tristan Payer, Tim Bergner, Pedro Hermosilla, Timo Ropinski","doi":"10.1111/jmi.70005","DOIUrl":"https://doi.org/10.1111/jmi.70005","url":null,"abstract":"<p><p>Deep learning (DL) has transformed image analysis, enabling breakthroughs in segmentation, object detection, and classification. However, a gap persists between cutting-edge DL research and its practical adoption in electron microscopy (EM) labs. This is largely due to the inaccessibility of DL methods for EM specialists and the expertise required to interpret model outputs. To bridge this gap, we introduce DeepEM Playground, an interactive, user-friendly platform designed to empower EM researchers - regardless of coding experience - to train, tune, and apply DL models. By providing a guided, hands-on approach, DeepEM Playground enables users to explore the workings of DL in EM, facilitating both first-time engagement and more advanced model customisation. The DeepEM Playground lowers the barrier to entry and fosters a deeper understanding of deep learning, thereby enabling the EM community to integrate AI-driven analysis into their workflows more confidently and effectively.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144528417","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":"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":"&lt;p&gt;&lt;p&gt;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, Laura Copeland, Giuseppe Di Caprio, Gail McConnell, Akhil Kallepalli","doi":"10.1111/jmi.70001","DOIUrl":"https://doi.org/10.1111/jmi.70001","url":null,"abstract":"<p><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":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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, P Bilski, M Sankowska","doi":"10.1111/jmi.70002","DOIUrl":"https://doi.org/10.1111/jmi.70002","url":null,"abstract":"<p><p>Background Remover (BGR) 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, BGR 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":" ","pages":""},"PeriodicalIF":1.5,"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, Thaina Alvarenga, Ruan Ingliton Feio, Cícero Brasileiro Mello, Gabriel Fidalgo, Katrine Paiva, Tayane Tanure, Liebert Parreiras Nogueira, Marcos Vinícius Colaço, Arissa Pickler, Marcelo Salabert Gonzalez, Patricia Azambuja, Giuliana Tromba, José Bento Pereira Lima, Ademir Xavier da Silva, Regina Cély Barroso","doi":"10.1111/jmi.70004","DOIUrl":"https://doi.org/10.1111/jmi.70004","url":null,"abstract":"<p><p>In this paper, in-line phase-contrast synchrotron microtomography was used to study the morphology of adult Aedes aegypti. 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 Aedes aegypti 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":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}