Journal of microscopy最新文献

{"title":"Deep learning assisted high-resolution microscopy image processing for phase segmentation in functional composite materials.","authors":"Ganesh Raghavendran, Bing Han, Fortune Adekogbe, Shuang Bai, Bingyu Lu, William Wu, Minghao Zhang, Ying Shirley Meng","doi":"10.1111/jmi.13413","DOIUrl":"https://doi.org/10.1111/jmi.13413","url":null,"abstract":"<p><p>In the domain of battery research, the processing of high-resolution microscopy images is a challenging task, as it involves dealing with complex images and requires a prior understanding of the components involved. The utilisation of deep learning methodologies for image analysis has attracted considerable interest in recent years, with multiple investigations employing such techniques for image segmentation and analysis within the realm of battery research. However, the automated analysis of high-resolution microscopy images for detecting phases and components in composite materials is still an underexplored area. This work proposes a novel workflow for FFT-based segmentation, periodic component detection and phase segmentation from raw high-resolution Transmission Electron Microscopy (TEM) images using a trained U-Net segmentation model. The developed model can expedite the detection of components and their phase segmentation, diminishing the temporal and cognitive demands associated with scrutinising an extensive array of TEM images, thereby mitigating the potential for human errors. This approach presents a novel and efficient image analysis approach with broad applicability beyond the battery field and holds potential for application in other related domains characterised by phase and composition distribution, such as alloy production.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803567","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":"Accelerating iterative ptychography with an integrated neural network.","authors":"Arthur R C McCray, Stephanie M Ribet, Georgios Varnavides, Colin Ophus","doi":"10.1111/jmi.13407","DOIUrl":"https://doi.org/10.1111/jmi.13407","url":null,"abstract":"<p><p>Electron ptychography is a powerful and versatile tool for high-resolution and dose-efficient imaging. Iterative reconstruction algorithms are powerful but also computationally expensive due to their relative complexity and the many hyperparameters that must be optimised. Gradient descent-based iterative ptychography is a popular method, but it may converge slowly when reconstructing low spatial frequencies. In this work, we present a method for accelerating a gradient descent-based iterative reconstruction algorithm by training a neural network (NN) that is applied in the reconstruction loop. The NN works in Fourier space and selectively boosts low spatial frequencies, thus enabling faster convergence in a manner similar to accelerated gradient descent algorithms. We discuss the difficulties that arise when incorporating a NN into an iterative reconstruction algorithm and show how they can be overcome with iterative training. We apply our method to simulated and experimental data of gold nanoparticles on amorphous carbon and show that we can significantly speed up ptychographic reconstruction of the nanoparticles.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803566","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":"Introduction to special issue on 'Microscopy Techniques'.","authors":"Stefan Linder","doi":"10.1111/jmi.13414","DOIUrl":"https://doi.org/10.1111/jmi.13414","url":null,"abstract":"","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772597","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":"Preparation and topographical studies of various biological specimens using alternate method to critical point drying: Scanning electron microscopy.","authors":"Najeeb Ullah, Darakhshan Guhar, Saifullah Khan","doi":"10.1111/jmi.13412","DOIUrl":"https://doi.org/10.1111/jmi.13412","url":null,"abstract":"<p><strong>Background: </strong>The major advantage of scanning electron microscope (SEM) in biological research is that one can examine the morphology and surface features of specimens at high resolution. Specimens may differ from individual cells grown in culture to solid tissues or entire organisms measuring several centimetres in size. It literally permits an 'in-depth' study of such specimens with great topography due to the incredible depth of field obtainable to the operator. Current study covers practical approaches of various biological samples' preparation and visualisation via scanning electron microscope.</p><p><strong>Methods: </strong>Alternate method of drying was employed over standard drying method; Critical Point Drying (CPD). Natural state of the microstructures of delicate specimens could be preserved by applying recommended reagents/ fixatives. Samples were treated with 2.5% w/w glutaraldehyde and reduced 1% Osmium tetroxide as primary and secondary fixatives. Samples were then serially dehydrated by graded ethanol (EtOH) and finally treated with chemical dehydrant Hexamethyldisilazane (HMDS).</p><p><strong>Results: </strong>Biological specimens, bacteria (Salmonella typhi and Staphylococcus aureus), bacterial crystal proteins, viruses (SARS-CoV-2), fungi (Aspergillus flavus), immune cells (monocytes) and invertebrates (Aedes aegypti), were studied and high-resolution images were captured. Detailed structural features were studied using high voltage electron beams (10-20 KV). Secondary electrons and backscattered electrons were detected to reveal detailed surface features of the specimens.</p><p><strong>Conclusion: </strong>Chemical critical drying was found to be an economic and yet effective method with less apparent deterioration of the surface features. The advantages of using a chemical dehydrant like Hexamethyldisilazane (HMDS) include ease of use, relative quickness, and less expense than a CPD. Same technique can be applied for different specimens with same results.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764181","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":"High-pressure freezing of mechanically stretched cells.","authors":"Edward Felder, Jan L Rüth, Bassam Abu-Omar, Martin Wohlwend, Paul Walther, Clarissa Read","doi":"10.1111/jmi.13411","DOIUrl":"https://doi.org/10.1111/jmi.13411","url":null,"abstract":"<p><p>High-pressure freezing (HPF) is an electron microscopy (EM) preparation technique with superb ultrastructural preservation. Combined with EM tomography it provides virtual EM serial sections with extraordinary spatial resolution. For HPF, cells are usually cultured on a rigid sapphire disc that provides a tight fit in the holding bracket of the HPF apparatus. Since we are using extensible elastic silicone membranes as a growth support to perform cell stretch experiments, we developed a method to clamp the stretched silicone membrane and place it instead of the sapphire disc into the HPF holding bracket. Compared to chemical fixation the HPF immobilised cells showed improved structural preservation, partly even on a molecular level. However, the outstanding quality of HPF immobilised cells on sapphire discs was not achieved. Moreover, regions with obvious freezing artefacts seemed to be more abundant in the HPF silicone membranes, probably caused by lower heat transfer rates of the silicone membrane during the HPF process. Taken together, we have shown that HPF immobilisation can be performed on growth supports different than sapphire discs. Since even stretched membranes can be used with the new method, also other unconventional growth supports should not pose a problem.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764179","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":"Advances, challenges, and applications of cryo-electron tomography workflows for three-dimensional cellular imaging of infectious pathogens.","authors":"Moara Lemos, Ingrid Augusto, Wanderley De Souza, Kildare Miranda","doi":"10.1111/jmi.13408","DOIUrl":"https://doi.org/10.1111/jmi.13408","url":null,"abstract":"<p><p>Cryo-electron tomography (cryo-ET) has become a powerful tool for visualising cellular structures at sub-nanometer resolution in their near-native state, offering unique insights into the molecular architecture of diverse biological systems, including infectious agents and their interactions with host cells. This paper reviews key methodologies and recent advancements in cryo-ET, with a particular focus on sample preparation of protozoan parasites and host cells. Topics covered include photopatterning for cell positioning on EM grids, vitrification techniques, whole-cell imaging, and cryo-FIB milling followed by cryo-ET. The manuscript also addresses how these approaches are providing valuable structural information on pathogens and pathogen-host interactions, which are critical for understanding mechanisms of pathogenesis and the development of therapeutic strategies. Additionally, we examine the principles and practical considerations of the multistep workflow, highlighting innovations such as integrated fluorescence microscopy (iFLM) within cryo-FIB SEM systems for improved target identification and lamella positioning. Challenges such as ion beam damage, sample thickness constraints, and the need for greater workflow automation are also discussed as areas for future improvement. As cryo-ET continues to evolve and deliver transformative insights into the molecular architecture of life, it inspires great hope for the development of future therapies against infectious diseases. LAY DESCRIPTION: Cryo-electron tomography (cryo-ET) is a special type of microscopy that allows researchers to look at the inside of cells in 3D, almost as if a hologram of the cell in its natural state was generated. This technique reveals molecular structures inside cells, allowing scientists to better understand how molecules and cellular components work together. To obtain such detailed images, biological samples need to be thin and frozen very quickly so that they remain undamaged and close to their natural state. One recent breakthrough involves using a tool called cryo-focused ion beam scanning electron microscopy (cryo-FIB SEM), which allows a thin slice of a frozen sample to be collected and then analysed using cryo-ET. In addition, photopatterning of support surfaces are being used to place cells in a strategic position for cryo-FIB SEM, and improved plunge freezing and high-pressure freezing methods have been developed to better preserve samples. Together, these techniques make it easier to reproducibly prepare high-quality samples for cryo-ET. These innovations allow capturing clearer and detailed images of cells, tissues, and even entire small organisms. Cryo-ET has led to important discoveries in biology, such as how proteins and other molecules interact within cells at the sub-nanometre scale. This technique holds great promise for revealing how life works at a molecular level, understanding diseases, and discovering new drugs.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143753093","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 phase magnitudes of open-source focused-probe 4D-STEM ptychography reconstructions.","authors":"Toma Susi","doi":"10.1111/jmi.13409","DOIUrl":"https://doi.org/10.1111/jmi.13409","url":null,"abstract":"<p><p>Accurate computational ptychographic phase reconstructions are enabled by fast direct-electron cameras with high dynamic ranges used for four-dimensional scanning transmission electron microscopy (4D-STEM). The availability of open software packages is making such analyses widely accessible, and especially when implemented in Python, easy to compare in terms of computational efficiency and reconstruction quality. In this contribution, I reconstruct atomic phase shifts from convergent-beam electron diffraction maps of pristine monolayer graphene, which is an ideal dose-robust uniform phase object, acquired on a Dectris ARINA detector installed in a Nion UltraSTEM 100 operated at 60 keV with a focused-probe convergence semi-angle of 34 mrad. For two different recorded maximum scattering angle settings, I compare a range of direct and iterative open-source phase reconstruction algorithms, evaluating their computational efficiency and tolerance to reciprocal-space binning and real-space thinning of the data. The quality of the phase images is assessed by quantifying the variation of atomic phase shifts using a robust parameter-based method, revealing an overall agreement with some notable differences in the absolute magnitudes and the variation of the phases. Although such variation is not a major issue when analysing data with many identical atoms, it does put limits on what level of precision can be relied upon for unique sites such as defects or dopants, which also tend to be more dose-sensitive. Overall, these findings and the accompanying open data and code provide useful guidance for the sampling required for desired levels of phase precision, and suggest particular care is required when relying on electron ptychography for quantitative analyses of atomic-scale electromagnetic properties.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143743239","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":"Hard X-ray spectromicroscopy of Ni-rich cathodes under in situ liquid heating conditions.","authors":"Gea T van de Kerkhof, Carmen Murphy, Shahul H Abdulrahman, Timothy Poon, Chris Hawkins, Mengliu Li, Angela E Goode, Julia E Parker, Manfred E Schuster","doi":"10.1111/jmi.13403","DOIUrl":"https://doi.org/10.1111/jmi.13403","url":null,"abstract":"<p><p>In situ microscopy involves imaging of samples under real reaction conditions. For electron microscopy, micro-electromechanical systems (MEMS) chips have previously been developed that can hold a liquid or gas inside the vacuum of the electron microscope, with electrical contacts that allow for heating or biasing of the sample. These chips have paved the way for high-resolution imaging of dynamic chemical reactions. Here, we report the use of such MEMS chips in an in-house developed setup for a hard X-ray nanoprobe, applied to Ni-rich cathode materials. We investigate the chemical and structural changes in nickel-rich cathodes upon exposure to electrolyte and under heating conditions using hard X-ray spectromicroscopy. As such, we find marked differences in the behaviour of pure LiNiO₂ compared to Co and Mn substituted material, NMC811. The use of hard X-ray spectromicroscopy allows for imaging and observation of: (i) the oxidation state of nickel, changing from Ni³⁺ to Ni²⁺, (ii) the effect of a preexisting fracture in the sample and (iii) the structural degradation of the sample during accelerated aging.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143709591","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":"Optimized single-beam modulation argon ion milling for TEM cross-sectional specimens of nanostructured interfaces.","authors":"Xiangtao Luo, Sujuan Ding, Haozhe Lu, Chuanhong Jin","doi":"10.1111/jmi.13406","DOIUrl":"https://doi.org/10.1111/jmi.13406","url":null,"abstract":"<p><p>High-quality transmission electron microscopy (TEM) specimens are critical for high-resolution imaging and conducting electron energy loss spectroscopy (EELS) analysis. However, fabricating cross-sectional TEM specimens with large, thin, and low-damage regions remains challenging, particularly with conventional mechanical polishing and Ar⁺ ion-beam milling methods. Here, we propose an optimised method based on Ar⁺ ion-beam milling that precisely maintains the consistency of the sample's thickness after mechanical polishing and fine-tunes Ar⁺ ion-beam milling parameters. Appropriately chosen milling parameters through real-time monitoring minimise the damaged layer's thickness, while optimised parameters reduce the redeposition of sputtered material. Applied to interfaces such as those between aligned carbon nanotube arrays (A-CNTs) and gate dielectrics key to next-generation nanoelectronics, we achieved samples with a 30 µm wide thin region, the thinnest area reaching 15 nm, preserving structural integrity and yielding a well-defined CNT-HfO₂ interface. Notably, redeposition was reduced from 44.4% to 6.6%, and single-beam modulation enabled these extensive thin regions, outperforming dual-beam methods.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700561","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":"Detecting charge transfer at defects in 2D materials with electron ptychography.","authors":"Christoph Hofer, Jacob Madsen, Toma Susi, Timothy J Pennycook","doi":"10.1111/jmi.13404","DOIUrl":"https://doi.org/10.1111/jmi.13404","url":null,"abstract":"<p><p>Electronic charge transfer at the atomic scale can reveal fundamental information about chemical bonding, but is far more challenging to directly image than the atomic structure. The charge density is dominated by the atomic nuclei, with bonding causing only a small perturbation. Thus detecting any change due to bonding requires a higher level of sensitivity than imaging structure and the overall charge density. Here we achieve the sensitivity required to detect charge transfer in both pristine and defected monolayer WS₂ using the high dose efficiency of electron ptychography and its ability to correct for lens aberrations. Excellent agreement is achieved with first-principles image simulations including where thermal diffuse scattering is explicitly modelled via finite-temperature molecular dynamics based on density functional theory. The focused-probe ptychography configuration we use also provides the important ability to concurrently collect the annular dark-field signal, which can be unambiguously interpreted in terms of the atomic structure and chemical identity of the atoms, independently of the charge transfer. Our results demonstrate both the power of ptychographic reconstructions and the importance of quantitatively accurate simulations to aid their interpretation.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673415","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}