Journal of microscopy最新文献

{"title":"Towards affordable biomedical imaging: Recent advances in low-cost, high-resolution optoacoustic microscopy.","authors":"Pavlos Kalitsounakis, Giannis Zacharakis, George J Tserevelakis","doi":"10.1111/jmi.13378","DOIUrl":"https://doi.org/10.1111/jmi.13378","url":null,"abstract":"<p><p>This short review discusses the recent developments in low-cost, high-resolution optoacoustic microscopy systems, integrating laser diodes for signal excitation, which are 20-40 times cheaper than the typically employed Q-switched nanosecond laser sources. The development of laser diode-based microscopes can substantially improve not only cost efficiency, but also multispectral capabilities, robustness, portability and overall imaging performance of the optoacoustic technique. To this end, we demonstrate relevant implementations in both time and frequency domain, highlighting their representative applications in biomedical research such as microvasculature imaging, oxygen saturation assessments, hybrid and multiview microscopy of model organisms and tissues and Doppler flow speed measurements. Finally, we analyse the benefits and limitations of each approach, identifying the respective application contexts where they achieve optimum performance.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801134","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.13322","DOIUrl":"https://doi.org/10.1111/jmi.13322","url":null,"abstract":"","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"297 1","pages":"1-2"},"PeriodicalIF":1.5,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13322","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142860671","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":"A comparison of super-resolution microscopy techniques for imaging tightly packed microcolonies of an obligate intracellular bacterium.","authors":"Alison J North, Ved P Sharma, Christina Pyrgaki, John Lim S Y, Sharanjeet Atwal, Kittirat Saharat, Graham D Wright, Jeanne Salje","doi":"10.1111/jmi.13376","DOIUrl":"10.1111/jmi.13376","url":null,"abstract":"<p><p>Conventional optical microscopy imaging of obligate intracellular bacteria is hampered by the small size of bacterial cells, tight clustering exhibited by some bacterial species and challenges relating to labelling such as background from host cells, a lack of validated reagents, and a lack of tools for genetic manipulation. In this study, we imaged intracellular bacteria from the species Orientia tsutsugamushi (Ot) using five different fluorescence microscopy techniques: standard confocal, Airyscan confocal, instant Structured Illumination Microscopy (iSIM), three-dimensional Structured Illumination Microscopy (3D-SIM) and Stimulated Emission Depletion Microscopy (STED). We compared the ability of each to resolve bacterial cells in intracellular clumps in the lateral (xy) axis, using full width half-maximum (FWHM) measurements of a labelled outer membrane protein (ScaA) and the ability to detect small, outer membrane vesicles external to the cells. Comparing the techniques readily available to us (above), 3D-SIM microscopy, in combination with the shortest-wavelength dyes, was found overall to give the best lateral resolution. We next compared the ability of each technique to sufficiently resolve bacteria in the axial (z) direction and found 3D-STED to be the most successful method for this. We then combined this 3D-STED approach with a custom 3D cell segmentation and analysis pipeline using the open-source, deep learning software, Cellpose to segment the cells and subsequently the commercial software Imaris to analyse their 3D shape and size. Using this combination, we demonstrated differences in bacterial shape, but not their size, when grown in different mammalian cell lines. Overall, we compare the advantages and disadvantages of different super-resolution microscopy techniques for imaging this cytoplasmic obligate intracellular bacterium based on the specific research question being addressed.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801127","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":"The photosensitive endoplasmic reticulum-chloroplast contact site.","authors":"Sara N Maynard, Lawrence R Griffing","doi":"10.1111/jmi.13377","DOIUrl":"https://doi.org/10.1111/jmi.13377","url":null,"abstract":"<p><p>The endoplasmic reticulum (ER) forms contact sites with the chloroplast. Exposing contact sites that contain both the chloroplast and the ER to localised high-fluence, wavelength specific, 405 nm violet light, hereinafter referred to as photostimulation, induces multiple, potentially interacting intra- and intercellular responses. The responses vary depending on the tissue type of the cell and the chloroplast. Photostimulating the ER-chloroplast contact sites in growing epidermal cells of the hypocotyl of Arabidopsis thaliana, produces a wave of cytoplasmic ionic calcium that traverses the cell, spreading radially to other cells around the circumference of the hypocotyl. A transient ER stress accompanies the calcium wave. These responses occur in older epidermal cells (5-8 days post-germination) with nonmotile chloroplasts tethered to the ER and the cell cortex but do not occur with motile or dividing chloroplasts. Dividing chloroplasts show a markedly different association with the ER, which forms a ring around the fission plane, similar to that of dividing mitochondria. Inhibition of calcium channels with lanthanum has no effect. Photostimulation of only the ER results in no ER stress and a calcium wave with a different spatiotemporal signature: delayed release and lower magnitude, with no accompanying ER stress response. Likewise, photostimulation of the chloroplast only, without the ER, produces no calcium wave or ER stress. General chloroplast photobleaching or restructuring caused by photostimulation is not the cause of this response; photostimulation with 488 nm of the same intensity and power as 405 nm photostimulation produces no change in cytosolic calcium levels. The pH of the ER decreases, indicating the involvement of ER ion transporters in the response. A wave of increased reactive oxygen species (ROS) in mitochondria and nuclei accompanies photostimulation. Together, these data support a model by which tethered ER-chloroplast contact sites constitute a unique subcellular photosensitive region and are part of an ER-mediated signalling network. Lay Abstract: The endoplasmic reticulum (ER) forms contact sites with the chloroplast. Shining violet (405 nm) light on the chloroplast with its associated ER produces a calcium wave through the cell that is communicated to other cells. This is correlated with a wave of transient denaturation of the luminal proteins of the ER (ER stress) and increased reactive oxygen species (ROS) in mitochondria. The wavelength dependence and precise cellular location of the light stimulation implies a novel way for plants to sense light. The movement of the response through the cell is consistent with the mediation of the response by a subcellular network, such as that formed by the ER.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779979","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":"Multicamera simultaneous total internal reflection and interference reflection microscopy.","authors":"Jeffrey O Spector, Jiayi Chen, Ewa Szczesna, Antonina Roll-Mecak","doi":"10.1111/jmi.13375","DOIUrl":"10.1111/jmi.13375","url":null,"abstract":"<p><p>Interference Reflection Microscopy (IRM) is an optical technique that relies on the interference between the reflected light from an incident beam as it passes through materials of different refractive indices. This technique has been successfully used to image microtubules, biologically important biofilaments with a diameter of 25 nm. However, it is often desirable to image both the microtubule and microtubule interacting proteins simultaneously. Here we present a simple modification to a standard multicolour total internal reflection fluorescence (TIRF) microscope that enables simultaneous high-speed IRM and single molecule TIRF imaging. Our design utilises a camera for each channel (IRM and TIRF) allowing independent optimisation of camera parameters for the two different modalities. We illustrate its application by imaging unlabelled microtubules and GFP-labelled end-binding protein EB1, which forms comets on the tips of polymerising microtubules. Our design is easily implemented, and with minimal cost, making it accessible to any laboratory with an existing fluorescence microscope.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769845","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":"Mechanical properties of bone cells studied by atomic force microscopy.","authors":"Xiaoqi Zhang, Zuobin Wang, Haiyue Yu, Zengren Tao, Wei Ji","doi":"10.1111/jmi.13373","DOIUrl":"https://doi.org/10.1111/jmi.13373","url":null,"abstract":"<p><p>Osteoblasts are the functional cells capable of bone formation in the bone microenvironment and play an important role in bone growth, development, and the maintenance of bone mass. The cells cultured in vitro are derived from preosteoblasts in tissues and possess the ability to divide and proliferate. Osteoblasts form the bone matrix by secreting collagen and other matrix proteins, which provides a foundation for the deposition of minerals such as calcium and phosphorus, ultimately resulting in the formation of hard bone tissue. Bone diseases affect the quality of life and the aging of the population. Bone diseases such as osteoporosis, fractures, bone tumours, and arthritis have a significant impact on quality of life, especially among the elderly population. These realities remind us that we should pay more attention to bone and joint health. Therefore, it is particularly important to study the imaging and characterisation of mechanical properties of bone cells, which provides a basis for the research of bone diseases in human beings.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769844","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":"Scanning transmission electron tomography to study virus assembly: Review for the retirement of Paul Walther.","authors":"Susanne Wieczorek, Jacomina Krijnse Locker","doi":"10.1111/jmi.13374","DOIUrl":"https://doi.org/10.1111/jmi.13374","url":null,"abstract":"<p><p>In this short and popular review, we summarise some of our findings analysing the replication cycles of large DNA viruses using scanning transmission electron tomography (STEM tomography) that we applied in the laboratory of Paul Walther. It is also a tribute to a very kind and expert scientist, who recently retired. Transmission electron microscopy (TEM), in particular cryo-EM, has benefited tremendously from recent developments in instrumentation. However, TEM imaging remains limited by the thickness of the specimen and classical thin-section TEM typically generates 2D representations of 3D volumes. Although TEM tomography can partly overcome this limitation, the thickness of the sample, the volume that can be analysed in 3D, remains limiting. STEM tomography can partly overcome this problem, as it allows for the analysis of thicker samples, up to 1 µm in thickness. As such, it is an interesting imaging technique to analyse large DNA viruses, some of which measure 1 µm or more, and which is the focus of our research interest.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142729703","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 whole human hair scalp fibres of varying curl: A micro-computed tomographic study.","authors":"Claire van den Berg, Nonhlanhla P Khumalo, Malebogo N Ngoepe","doi":"10.1111/jmi.13365","DOIUrl":"https://doi.org/10.1111/jmi.13365","url":null,"abstract":"<p><p>Scalp hair is a key feature of humans and its variability has been the subject of a broad range of studies. A small subset of these studies has focused on geometric quantification of human scalp hair fibres, however the use of race- and ethnicity-based classification systems makes it challenging to draw objective conclusions about fibre variability. Furthermore, sample preparation techniques for micro-imaging studies often alter the original form of hair fibres. This study sought to determine which of the commonly reported descriptors could be resolved using micro-computed tomography (micro-CT) for fibres of varying curl. Images obtained from micro-CT were used to reconstruct three-dimensional images that were then analysed. The study also explored the capabilities and limitations of micro-CT as an imaging modality by comparing and cross-validating findings with those obtained from scanning electron microscopy (SEM) and laser micrometry. The former deals with surface imaging while the latter deals with cross-sectional measurements. Micro-CT was found to be highly effective at resolving cross-sectional ellipsoidal parameters, but performed more poorly than SEM in reconstructing surface level details at a 2 <math> <semantics><mrow><mi>μ</mi> <mi>m</mi></mrow> <annotation>$umutext{m}$</annotation></semantics> </math> resolution. The technique was, however, able to reveal the presence of the medulla in type VI (high curl) hair fibres. When compared with high curl fibres, greater intra-fibre variability was observed for the low and medium curl fibres, highlighting the importance more objective classification systems.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675958","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":"Diagnostic electron microscopy in human infectious diseases - Methods and applications.","authors":"Michael Laue","doi":"10.1111/jmi.13370","DOIUrl":"10.1111/jmi.13370","url":null,"abstract":"<p><p>Diagnostic electron microscopy (EM) is indispensable in all cases of infectious diseases which deserve or profit from the detection of the entire pathogen (i.e. the infectious unit). The focus of its application has shifted during the last decades from routine diagnostics to diagnostics of special cases, emergencies and the investigation of disease pathogenesis. While the focus of application has changed, the methods remain more or less the same. However, since the number of cases for diagnostic EM has declined as the number of laboratories that are able to perform such investigations, the preservation of the present knowledge is important. The aim of this article is to provide a review of the methods and strategies which are useful for diagnostic EM related to infectious diseases in our days. It also addresses weaknesses as well as useful variants or extensions of established methods. The main techniques, negative staining and thin section EM, are described in detail with links to suitable protocols and more recent improvements, such as thin section EM of small volume suspensions. Sample collection, transport and conservation/inactivation are discussed. Strategies of sample examination and requirements for a proper recognition of structures are outlined. Finally, some examples for the actual application of diagnostic EM related to infectious diseases are presented. The outlook section will discuss recent trends in microscopy, such as automated object recognition by machine learning, regarding their potential in supporting diagnostic EM.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668281","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":"Brain tissue classification in hyperspectral images using multistage diffusion features and transformer.","authors":"Neetu Sigger, Tuan T Nguyen, Gianluca Tozzi","doi":"10.1111/jmi.13372","DOIUrl":"https://doi.org/10.1111/jmi.13372","url":null,"abstract":"<p><p>Brain surgery is a widely practised and effective treatment for brain tumours, but accurately identifying and classifying tumour boundaries is crucial to maximise resection and avoid neurological complications. This precision in classification is essential for guiding surgical decisions and subsequent treatment planning. Hyperspectral (HS) imaging (HSI) is an emerging multidimensional optical imaging method that captures detailed spectral information across multiple wavelengths, allowing for the identification of nuanced differences in tissue composition, with the potential to enhance intraoperative tissue classification. However, current frameworks often require retraining models for each HSI to extract meaningful features, resulting in long processing times and high computational costs. Additionally, most methods utilise the deep semantic features at the end of the network for classification, ignoring the spatial details contained in the shallow features. To overcome these challenges, we propose a novel approach called MedDiffHSI, which combines diffusion and transformer techniques. Our method involves training an unsupervised learning framework based on the diffusion model to extract high-level and low-level spectral-spatial features from HSI. This approach eliminates the need for retraining of spectral-spatial feature learning model, thereby reducing time complexity. We then extract intermediate multistage features from different timestamps for classification using a pretrained denoising U-Net. To fully explore and exploit the rich contextual semantics and textual information hidden in the extracted diffusion feature, we utilise a spectral-spatial attention module. This module not only learns multistage information about features at different depths, but also extracts and enhances effective information from them. Finally, we employ a supervised transformer-based classifier with weighted majority voting (WMV) to perform the HSI classification. To validate our approach, we conduct comprehensive experiments on in vivo brain database data sets and also extend the analysis to include additional HSI data sets for breast cancer to evaluate the framework performance across different types of tissue. The results demonstrate that our framework outperforms existing approaches by using minimal training samples (5%) while achieving state-of-the-art performance.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675063","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}