Journal of microscopy最新文献

{"title":"GloBIAS survey results - An insight into the global bioimage analysis community.","authors":"Laura R de la Ballina, Christa G Walther, Nicholas D Condon, Alessandro A Felder, Martin Schätz, Bettina Schmerl, Ko Sugawara, Clara Prats, Anna Klemm, Kota Miura, Paula Sampaio, Christian Tischer, Shuichi Onami, Rocco D'Antuono, Beth A Cimini, Robert Haase, Agustin A Corbat, Florian Levet","doi":"10.1111/jmi.70153","DOIUrl":"https://doi.org/10.1111/jmi.70153","url":null,"abstract":"<p><p>There is a global need for bioimage analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of biological images. Turning these data into scientific discoveries requires scientists with effective data management skills and knowledge of state-of-the-art image processing and data analysis, in other words, bioimage analysts. The Global BioImage Analysts' Society (GloBIAS) aims to enhance the profile of bioimage analysts as a key role in science and research. To better understand the needs and geographical representation of the BIA community, a worldwide survey was conducted, and 290 responses were collected across people from all career stages and continents. The survey underscores a strong interest of the BIA community in the activities proposed by GloBIAS to address shortcomings in work environment, funding, and scientific activities, and the enthusiasm of the community to actively contribute to the growth and sustainability of GloBIAS as a scientific society.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148592249","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":"Simplex-based model for nanoparticle grain identification in four-dimensional scanning transmission electron microscopy data","authors":"Wei Liu,&nbsp;Roberto dos Reis,&nbsp;Chad A. Mirkin,&nbsp;Vinayak P. Dravid,&nbsp;Wei Chen,&nbsp;Daniel W. Apley","doi":"10.1111/jmi.70126","DOIUrl":"10.1111/jmi.70126","url":null,"abstract":"<p>Grain identification in polycrystalline nanoparticles, for example, determining which crystal phases are present at each spatial location, is fundamental to materials characterisation. This is particularly challenging when grains overlap extensively, as commonly occurs in four-dimensional scanning transmission electron microscopy (4D-STEM) datasets. We propose a simplex-based model (SBM) in which each simplex vertex represents the diffraction pattern (DP) of a pure grain, and the simplex edges and interior represent overlapping grains. Our SBM grain identification algorithm operates on the Bragg disk (BD) data matrix distilled from the 4D-STEM data to identify the grain membership at each scan position, together with a BD feature matrix whose columns represent the DPs for each constituent grain, which is important for identifying the crystal structure of each grain. We solve the model using a two-stage algorithm. In Stage 1, we adapt a linear mixing algorithm to estimate an initial BD feature matrix whose columns represent DPs of potentially overlapping grains. Our Stage 2 algorithm incorporates sparsity considerations to transform the initial BD feature matrix so that its columns represent DPs of pure grains. Using simulated datasets with various grain configurations, we demonstrate that SBM recovers both the BD feature matrix and membership maps more accurately than existing methods, even when a grain lacks any pure region and completely overlaps with other grains.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 2","pages":"194-215"},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70126","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148149978","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":"Tubule and microbranch variations in human dentine: A quantitative 3D study with serial block-face scanning electron microscopy","authors":"Bethany Harding,&nbsp;Patricia Goggin,&nbsp;James Thompson,&nbsp;Behrad Mahmoodi,&nbsp;Katy Rankin,&nbsp;Philipp Schneider,&nbsp;Richard Cook","doi":"10.1111/jmi.70123","DOIUrl":"10.1111/jmi.70123","url":null,"abstract":"<p><b>Objective</b>: Microbranches exist within dentine, providing a network of fluid filled connections between tubules. This study used serial block-face scanning electron microscopy to generate 3D volumes of dentine from different tooth locations, allowing for investigations of the microbranch morphology, the microbranch network characteristics and regional variations in the tooth.</p><p><b>Methods</b>: Three human teeth were sectioned to generate 21 dentine samples extracted from 7 identical regions of interest around the tooth. Serial block-face scanning electron microscopy was performed using a pixel size of 10 nm, a slice thickness of 50 nm, and a field of view of 20.48 µm × 20.48 µm. Tubules and microbranches were automatically segmented and the following quantified: tubule diameter and density; microbranch diameter, density, and connectivity; tissue porosity.</p><p><b>Results</b>: The microbranches were successfully captured at sufficient resolution to create a 3D volume from sequential 2D images. The microbranches move tortuously through the intertubular dentine and travelled a variety of distances before connecting to other tubules. The microbranch density varied by location, with more found in areas of lower tubule density. Microbranches significantly increased tissue porosity (<i>p</i> &lt; 0.001). Microbranch diameter did not vary regionally, with most approximately 140–210 nm, regardless of sample location. Tubule density and diameter varied radially—both largest closest to the pulp cavity, then decreasing to the dentinoenamel junction.</p><p><b>Conclusions</b>: This study provides new three-dimensional insight into the morphology and network of the dentinal microbranch network, demonstrating a variability in the density of the microbranches with location around the tooth and a significant increase in tissue porosity.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 2","pages":"171-183"},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70123","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148005538","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":"Dynamical simulation of on-axis transmission Kikuchi and spot diffraction patterns, based on accurate diffraction geometry calibration","authors":"Tianbi Zhang,&nbsp;Raynald Gauvin,&nbsp;Aimo Winkelmann,&nbsp;T. Ben Britton","doi":"10.1111/jmi.70119","DOIUrl":"10.1111/jmi.70119","url":null,"abstract":"<p>Transmission Kikuchi diffraction in the scanning electron microscope has gained popularity as a materials characterisation technique for its high throughput and nanometre-level spatial resolution. While conventional diffraction pattern analysis routines focus on Kikuchi bands on the diffraction patterns, the full physical picture of electron scattering and diffraction pattern formation is more complex. Analysis that accounts for additional diffraction features such as diffraction spots and excess-deficiency effects should provide more robust and accurate indexing, if they can be incorporated in pattern indexing or simulation routines. A more accurate understanding of their physics of formation and geometry is required to enable this change. In this work, we demonstrate geometric and full contrast dynamical simulation of on-axis transmission Kikuchi patterns, based on experimental patterns captured using a modular, direct electron detector-based set-up in the scanning electron microscope. First, a diffraction geometry calibration routine is proposed based on the electron channelling pattern of the direct electron detector. This allows us to accurately account for the position of diffraction spots in both geometric and dynamical simulations with good agreement with experimental patterns. Further, by introducing appropriate weight factors, simulation of incoherent diffuse intensity, and calculation of the energy spectra of diffracted electrons, simulated patterns can be obtained which accurately capture the many diffraction features on experimental patterns. Workflows and findings of this work can be used to improve pattern indexing routines, as well as the understanding of the physical processes in the formation of on-axis transmission Kikuchi patterns.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 2","pages":"139-153"},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70119","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147972941","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":"Comment on ‘A novel experimental platform to monitor solid/water interfaces under freeze–thaw cycles’","authors":"Maajid Mohi Ud Din Malik,&nbsp;Abhay Saraf,&nbsp;Milind P Bhrushundi","doi":"10.1111/jmi.70135","DOIUrl":"10.1111/jmi.70135","url":null,"abstract":"","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 2","pages":"229-230"},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148226069","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":"Presynaptic actin nanostructures: A reproducibility case study.","authors":"Rensu P Theart, Florian Levet, Paul Hernández-Herrera, Christophe Leterrier, Laura R de la Ballina","doi":"10.1111/jmi.70138","DOIUrl":"https://doi.org/10.1111/jmi.70138","url":null,"abstract":"<p><p>In an effort to assess the reproducibility of bioimage analyses in current publications, we took part in a Global BioImage Analysts' Society (GloBIAS) initiative to try and reproduce results from published articles. We attempted to reproduce core findings from Bingham et al. (2023), who investigate the actin organisation in presynaptic structures by using diffraction-limited and super-resolution microscopy. While the original paper unveiled novel biological insight, it lacked sufficient detail in the bioimage analysis methodology, limiting the depth of reproducibility we could achieve. Through frequent contacts with the corresponding author, we were able to replicate qualitative aspects of the analysis of actin nanostructures in bead-induced presynapses. We performed image reconstruction from super-resolution microscopy data, automatic image registration and visual inspection, followed by manual annotation of structures of interest in approximately 35 images. From this exercise, we provide concrete evidence that key practises such as sharing of example datasets, depositing manual annotations and documenting manual decision criteria and consensus procedures are essential for making bioimage analysis workflows reproducible. Our experience further highlights that transparent data sharing, adherence to bioimage analysis standards, and close collaboration between experimentalist and bioimage analysis specialists are critical to ensure the reproducibility of today's complex biological imaging studies.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148579116","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 novel scanning tunnelling microscope head with a double-piezo-tube nested scanner for operation in a vibrational magnet","authors":"Shuai Dong,&nbsp;Jihao Wang,&nbsp;Dan Wu,&nbsp;Yubin Hou,&nbsp;Qingyou Lu","doi":"10.1111/jmi.70124","DOIUrl":"10.1111/jmi.70124","url":null,"abstract":"<p>Coarse stepping motor and imaging scanner are the most important components of the scanning tunnelling microscope (STM). In traditional STMs, a single small-sized piezoelectric tube is fixed directly to the motor and used as the imaging scanner, the small-sized scanner can only provide a small imaging area. As a result, those STMs need equipped with <i>X</i>–<i>Y</i> piezo stage to move sample. While the noise generated from coarse stepping motor and <i>X</i>–<i>Y</i> piezo stage, as well as the complex structure will greatly reduce the STM's imaging stability. In this paper, we present an independent scanner structure featuring a double-piezo-tube nested design. In this design, both two piezoelectric tubes can be responsible for adjusting the tip-sample distance; the external scan tube can be used to adjust the position of the sample. The small tip-sample mechanical loop and compact structure of the scanner ensure the high imaging stability of the new STM. Finally, we constructed a non-magnetic STM head based on above novel scanner. High-quality atomic images of the highly ordered pyrolytic graphite (HOPG) and low drift rates in both <i>X</i>–<i>Y</i> plane and <i>Z</i> directions were obtained at room temperature, demonstrating the high imaging stability of our new STM even at 300 K. Additionally, atomic images and the <i>dI</i>/<i>dV</i> spectra of NbSe₂ obtained at 1.7 K, as well as the atomic images of HOPG obtained at changing magnetic fields from 0 T to 12 T in a vibrational magnet, proving new STM's high stability under low temperature and high magnetic fields.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 2","pages":"184-193"},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148005501","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":"Flash electropolishing for TEM: Reducing FIB-induced defects in tungsten with protocols for new materials#","authors":"Yan-Ru Lin,&nbsp;Weicheng Zhong,&nbsp;Sabrina E. Calzada,&nbsp;Timothy G. Lach,&nbsp;Lauren J. Nuckols,&nbsp;Chad M. Parish,&nbsp;Steven J. Zinkle,&nbsp;M. Grace Burke","doi":"10.1111/jmi.70122","DOIUrl":"10.1111/jmi.70122","url":null,"abstract":"<p>Focused ion beam (FIB) milling has become the dominant approach for site-specific transmission electron microscopy (TEM) specimen preparation; however, FIB damage remains a critical limitation for reliable microstructural characterisation, particularly in radiation effects studies. Tungsten is especially susceptible to FIB damage due to its high nuclear stopping power, which promotes the formation and strong diffraction contrast of FIB-induced ‘black spot’ defects that are indistinguishable from very fine irradiation-induced loops/defects resulting from low to intermediate temperature neutron irradiation. In this work, flash electropolishing is systematically evaluated as a post-FIB treatment for minimising preparation-induced artefacts for TEM analysis of tungsten-based alloys. Using a range of non-, ion-, and neutron-irradiated tungsten materials, the effectiveness of flash electropolishing has been assessed through direct comparison with conventional FIB and plasma-FIB preparation including low-energy Ga, Ar, Xe ion cleaning. The results demonstrate that flash electropolishing effectively removes FIB-damaged layers and ‘black spot’ defects, thereby enabling reliable observation of irradiation-induced dislocation structures. Key processing parameters governing flash electropolishing quality – including lamella thickness, applied voltage, polishing duration, electrolyte chemistry, and cathode geometry – have been systematically evaluated, and clear criteria were established for determining when flash electropolishing is required to ensure reliable microstructural analysis. This work also provides practical guidance for implementing flash electropolishing as an artefact-controlled specimen-preparation approach for TEM characterisation of FIB-produced specimens. The systematic protocol can be extended to other, non-tungsten materials.</p><p><b>LAY DESCRIPTION</b>: Flash electropolishing is demonstrated as an effective post-FIB treatment for removing preparation-induced damage in tungsten TEM specimens, including FIB-induced ‘black spot’ defects that can obscure irradiation microstructures. Through systematic comparison with conventional and plasma-FIB methods across irradiated and non-irradiated tungsten alloys, key processing parameters and reliability criteria are established. The work provides a practical, artefact-controlled preparation protocol for accurate radiation-damage characterisation and offers a broadly adaptable strategy for other material systems.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 2","pages":"154-170"},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148005560","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":"TOC - Issue Information","authors":"","doi":"10.1111/jmi.70144","DOIUrl":"https://doi.org/10.1111/jmi.70144","url":null,"abstract":"","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.70144","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148553347","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":"An affordable fiducial marker strategy for reliable autofocus in long-term live microscopy","authors":"Ilyas Djafer-Cherif,&nbsp;Bartlomiej Waclaw","doi":"10.1111/jmi.70127","DOIUrl":"10.1111/jmi.70127","url":null,"abstract":"<p>Long-term time-lapse imaging of biological samples requires correcting for focal drift, which would otherwise gradually push the sample out of focus. We present a software-based method that eliminates this time-dependent blur using only a motorised <i>Z</i>-drive, with no additional hardware. The method relies on imaging marks made on the side of the coverslip opposite to the sample. We provide a Beanshell script implementation, evaluate its performance across multiple objectives, and benchmark it against a hardware autofocus system, finding comparable results. Finally, we demonstrate its effectiveness in live imaging of growing bacterial colonies.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"303 2","pages":"216-228"},"PeriodicalIF":1.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148218162","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}