Journal of microscopy最新文献

{"title":"The reproducibility gap in graph neural network workflows for cell dynamics: A checklist-driven case study.","authors":"Martin Schätz, Ko Sugawara","doi":"10.1111/jmi.70139","DOIUrl":"https://doi.org/10.1111/jmi.70139","url":null,"abstract":"<p><p>As part of a Global BioImage Analysts' Society (GloBIAS) initiative, we evaluated the reproducibility of a Graph Neural Network (GNN) study on cell dynamics using structured, community-developed checklists from the Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi) initiative. Notably, these checklists were published after the 2022 Target Paper, meaning our assessment is necessarily retrospective. Our assessment revealed a gap between recent reporting standards and practical execution. Reproduction attempts across multiple environments confirmed deficiencies, including the absence of explicit image metadata (pixel size and timestamps), which limits quantitative interpretation. Furthermore, the absence of a software container, which was typical for the time of publication and the incomplete dependency list, necessitated complex manual environment configuration, increasing the barrier to entry. This experience highlights the contrast between the reproducibility expectations at the time and newer standards achieved by minimal compliance and true functional access. We conclude by presenting a detailed discussion of the broader implications for the quantitative biology community and propose actionable recommendations including robust environment containerisation and standardised data deposition to ensure complex computational workflows become scientifically sound and reusable resources. This retrospective case study evaluates a legacy computational paper against modern reproducibility framework, not to critique past non-compliance, but to extract actionable lessons for future research standards.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148301734","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":"Transmission electron microscopy characterisation of Spirulina bioplastics","authors":"Sourena Azidhak,&nbsp;Douglas J. Taatjes,&nbsp;Ian R. Campbell,&nbsp;Eleftheria Roumeli,&nbsp;Linda S. Schadler","doi":"10.1111/jmi.70093","DOIUrl":"10.1111/jmi.70093","url":null,"abstract":"<p>Plastic pollution is impacting global ecosystem health. Bioplastics made from unprocessed biomass, including whole or fragmented tissues, are one potential solution. They are biodegradable and exhibit competitive mechanical performance. Seaweed and microalgae have gained popularity over the last decade as bioplastic feedstocks due to their abundance and ease of cultivation. To grasp the complexity of transforming biomatter into bioplastics and to optimise their performance, it is essential to develop processing–structure–property relationships. Transmission electron microscopy can be used to observe the morphology of bioplastics; however, current infiltration techniques are designed for biomaterials in their natural state, and harsh reagents can cause artefacts in bioplastic structure. This paper examines four different fixation methods for Spirulina bioplastics and investigates the impact of fixative, contrasting, dehydration, and resin embedding on Spirulina ultrastructure before and after bioplastic transformation. Our study suggests that the key to preserving bioplastic morphology is to prepare the specimen for electron microscopy by exposing it to gas-phase infiltration.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 1","pages":"101-119"},"PeriodicalIF":1.9,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70093","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147690720","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":"Correction to ‘Building capacity in imaging data management’","authors":"","doi":"10.1111/jmi.70117","DOIUrl":"10.1111/jmi.70117","url":null,"abstract":"<p>Velasquez, S. M., Fletcher, G., Burel, … Küpcü Yoldaş, A. (2026). Building capacity in imaging data management. <i>Journal of Microscopy</i>, 1–12. https://doi.org/10.1111/jmi.70078</p><p>Josh Moore was inadvertently omitted from the author list. He is now added as one of the authors of this publication.</p><p>We apologise for this error.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147930505","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":"Correction to “Exploring poly-L-lysine-based particle capture for atomic force microscopy studies of extracellular vesicles”","authors":"","doi":"10.1111/jmi.70118","DOIUrl":"10.1111/jmi.70118","url":null,"abstract":"<p>L. Conti, A. Ridolfi, A. Borup, M. J. C. van Herwijnen, P. Nejsum, M. H. M. Wauben, C. Albonetti, F. Valle, M. Brucale (2026) Exploring poly-L-lysine-based particle capture for atomic force microscopy studies of extracellular vesicles. <i>Journal of Microscopy</i>, <i>302</i>(1), 100-110. https://doi.org/10.1111/jmi.70060</p><p>The first two items in the affiliations list are presented in the wrong order and contain incorrect institutional details; the corresponding author has been assigned an incorrect affiliation. The correct affiliations and corresponding author details are provided below:</p><p>¹Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Consiglio Nazionale delle Ricerche (CNR), Bologna, Italy.</p><p>²Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), University of Florence, Florence, Italy.</p><p>³Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.</p><p>⁴Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.</p><p><b>Correspondence</b>:</p><p>M. Brucale, Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Consiglio Nazionale delle Ricerche (CNR), Bologna, Italy.</p><p>Email: <span>[email protected]</span></p><p>We apologise for this error.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70118","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147930559","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":"Extraction replica method from thinned transmission electron microscopy samples without floating off carbon films: A case study on reduced activation steel","authors":"Jack Haley,&nbsp;Alex Dickinson-Lomas,&nbsp;Qianyi Sun,&nbsp;David Bowden","doi":"10.1111/jmi.70113","DOIUrl":"10.1111/jmi.70113","url":null,"abstract":"<p>A recipe for producing carbon extraction replicas from twin-jet electropolished disks is described. This technique allows tracking the analysed region with respect to the bulk sample. An example use of the method as applied to a reduced activation ferritic martensitic (RAFM) steel, ‘UK-RAFM’, is reported. The RAFM steel described originates from a ∼5 tonne heat produced via electric-arc furnace (EAF) and was intended to match Eurofer-97 in chemistry. Here, a detailed analysis of the precipitates within the UK-RAFM is provided, with particular emphasis to show the variability in chemistry of second-phase precipitates (SPPs). Comparisons to literature reported compositions of Eurofer-97 SPPs indicate they are in reasonable agreement; comparisons are also made against thermodynamic models.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 1","pages":"88-100"},"PeriodicalIF":1.9,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70113","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147972931","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":"Closer to the native state: Sandwich freezing and freeze-substitution of microorganisms, cultured cells, and animal and plant tissues for electron microscopy","authors":"Masashi Yamaguchi,&nbsp;Katsuyuki Uematsu,&nbsp;Toshikatsu Kuramoto,&nbsp;Shinichi Ohno,&nbsp;Hiroji Chibana,&nbsp;Azusa Takahashi-Nakaguchi","doi":"10.1111/jmi.70096","DOIUrl":"10.1111/jmi.70096","url":null,"abstract":"<p>Since the invention of the electron microscope, morphologists have developed numerous techniques to visualise the native ultrastructure of biological cells and tissues. Although conventional chemical fixation followed by room temperature dehydration remains widely used, it often fails to preserve native structures, leading to distortion and leakage of cellular components. In contrast, cryofixation combined with freeze substitution offers a superior alternative, producing micrographs that more accurately reflect native ultrastructure.</p><p>We have developed a ‘sandwich freezing method’ for rapid cryofixation, in which small biological specimens are placed between two copper disks, rapidly frozen by plunging into melting propane cooled with liquid nitrogen, then freeze-substituted in acetone containing osmium tetroxide at low temperature, and finally embedded in epoxy resin.</p><p>This technique yields exquisitely preserved, near-native ultrastructure in living microorganisms and plant tissues. For cultured cells and animal tissues, prefixation with glutaraldehyde prior to sandwich freezing results in even more native-like preservation compared to specimens frozen without fixation. We propose that glutaraldehyde prefixation prevents the immediate distortion and ultrastructural changes that occur upon removal of cells and tissues from their culture medium or host organism. Importantly, glutaraldehyde rapidly immobilises cellular components without altering cellular architecture.</p><p>We recommend the routine application of the sandwich freezing–freeze substitution technique to achieve ultrastructural preservation that is as close to the native state as possible in electron microscopy.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 1","pages":"21-36"},"PeriodicalIF":1.9,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147773904","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":"Assessing the reproducibility of a bioimage analysis workflow characterising tissue flow in Drosophila.","authors":"Mélodie Ambroset, Cesar Augusto Valades-Cruz, Libert Brice Tonfack, Rocco D'Antuono, Caterina Fuster-Barceló","doi":"10.1111/jmi.70125","DOIUrl":"https://doi.org/10.1111/jmi.70125","url":null,"abstract":"<p><p>Reproducibility challenges in bioimage analysis are common. The proliferation of tools and workflows creates a complex ecosystem that is difficult to reproduce without deliberate, explicit reporting and support. We assess the reproducibility of Gehrels et al.(2023) as a representative bioimage analysis workflow. We do not evaluate the biological claims; instead, we examine the reproducibility of the bioimage analysis methods used and the implications for current peer-review practices in the field. Although some data were deposited in the BioImage Archive and code was available on GitHub, the materials were insufficient to completely reproduce the analysis. Moreover, the repository lacked the configuration to enable straightforward replication of the workflow or results. This case study highlighted how incomplete reporting can significantly hinder the reproduction of bioimage analysis workflows. Because scientific progress relies on verifiable replications, insufficiently reproducible results can erode confidence in the scientific record.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148271912","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":"Imaging around the globe: Tailoring microscopy outreach to local research demands","authors":"Anja Schmidt,&nbsp;Harikrushnan Balasubramanian,&nbsp;Shinya Komoto,&nbsp;Leonel Malacrida,&nbsp;Clara Prats,&nbsp;Michael Reiche,&nbsp;Jesse Aaron,&nbsp;Teng-Leong Chew","doi":"10.1111/jmi.70087","DOIUrl":"10.1111/jmi.70087","url":null,"abstract":"<p>The global microscopy community has made wide efforts in imaging technology dissemination, especially to lower- and middle-income countries. Yet, many efforts have not fully realised their aim of increased, sustained microscopy utilisation. To guide future outreach initiatives towards more positive results, we analysed over 2300 unique applications across seven recent international microscopy workshops. We found significant differences in research priorities, as well as in microscopy experience and applications between lower- and higher-income regions. We discuss the importance of tailoring technology dissemination, training curricula, and capacity-building to these regional variations.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 1","pages":"53-59"},"PeriodicalIF":1.9,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147645632","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":"RNA-based CLEM (RCLEM) bridging RNA localisation and ultrastructural mapping in 3D","authors":"Daan Verhaege,&nbsp;Lore Van Acker,&nbsp;Camille Wagner,&nbsp;Yentl Van den Berghe,&nbsp;Jérémy Verbeke,&nbsp;Martin Guilliams,&nbsp;Anna Kremer,&nbsp;Lien Van Hoecke,&nbsp;Roosmarijn E Vandenbroucke","doi":"10.1111/jmi.70105","DOIUrl":"10.1111/jmi.70105","url":null,"abstract":"<p>Spatial transcriptomics and in situ hybridisation techniques have become essential for contextualising single-cell RNA sequencing (scRNA-seq) data by mapping cell type– and state–specific mRNA expression within intact tissues. Beyond validating scRNA-seq predictions, these spatial methods provide critical insight into the localisation of specific cell types and their spatial relationships with neighbouring cells. However, current approaches rely on light microscopy (LM), which, despite advances, lacks the resolution needed to resolve detailed cell morphology or subcellular RNA localisation in situ. While correlative imaging methods can enhance spatial context, RNA detection remains limited by the optical constraints of LM. To overcome these challenges, we developed a three-dimensional RNA-based correlated light and electron microscopy (RCLEM) workflow. This method integrates RNA labelling with serial block-face scanning electron microscopy (SBF-SEM), allowing high-resolution 3D visualisation of RNA molecules within their ultrastructural environment. We optimised the RNA labelling protocol for thick, whole-mount tissues by fine-tuning detergent conditions to preserve ultrastructure while maintaining probe accessibility. This RCLEM approach offers several advantages over protein-based correlative methods, including robust detection with nucleotide probes and independence from antibody optimisation or fixation-sensitive epitopes. Applied to choroid plexus (ChP) and liver tissue, this workflow enabled precise 3D correlation between mRNA expression and EM features, supporting detailed morphological characterisation of rare scRNA-seq–defined cell subtypes. This protocol is broadly applicable to other complex tissues and provides a powerful platform for integrative, high-resolution spatial transcriptomic analyses that bridge gene expression with ultrastructure.</p><p><b>LAY DESCRIPTION</b>: To overcome the resolution limits of current spatial transcriptomics, we developed a 3D RNA-based correlated light and electron microscopy (RCLEM) workflow. By integrating RNA labelling with scanning electron microscopy, this method enables high-resolution 3D visualisation of mRNA within its ultrastructural environment in thick tissues. Validated in choroid plexus and liver, our antibody-independent RCLEM approach provides a broadly applicable platform bridging gene expression and precise cellular morphology for advanced spatial analyses.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 1","pages":"120-131"},"PeriodicalIF":1.9,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70105","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147930483","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":"From EM to AI: Multiscale imaging of the secretory pathway with insights from plant cells","authors":"Charlotte Pain,&nbsp;Emily Farley","doi":"10.1111/jmi.70115","DOIUrl":"10.1111/jmi.70115","url":null,"abstract":"<p>The secretory pathway is a central and evolutionarily conserved feature of eukaryotic cells, responsible for protein and lipid trafficking, membrane biogenesis, signalling, and cellular homeostasis. Its complexity, dynamic behaviour, and nanoscale organisation have made it a longstanding target of microscopy-driven investigation. In this review, we trace the parallel evolution of our understanding of the secretory pathway and imaging technologies, with a particular emphasis on plant cells, where unique architectural and functional features have challenged and enriched mechanistic models. We highlight the foundational role of electron microscopy (EM) in defining the ultrastructural organisation of secretory organelles and establishing directional models of intracellular transport, followed by the fluorescence microscopy revolution that enabled direct visualisation of cargo flux and organelle dynamics in living cells. The advent of super-resolution fluorescence techniques bridged the long-standing resolution gap between light microscopy and EM, revealing nanoscale compartmentalisation, membrane contact sites, and trafficking intermediates previously inaccessible in living cells. More recently, the integration of functional assays, optogenetics, and artificial intelligence-driven segmentation, denoising, and adaptive imaging now enables quantitative and high-throughput analysis of secretory architecture. Together, these advances have transformed the secretory pathway from a static morphological concept into a dynamic, increasingly mechanistically defined system. We conclude by discussing emerging integrative strategies, particularly correlative and AI-enhanced approaches that promise to unify ultrastructural precision with molecular specificity and temporal resolution in future studies of endomembrane organisation.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 1","pages":"3-20"},"PeriodicalIF":1.9,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70115","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147930473","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}