Journal of microscopy最新文献_第9页

Flexible implementation of modulated localisation microscopy based on DMD 基于 DMD 的调制定位显微镜的灵活实施。

IF 2 4区工程技术

Journal of microscopy Pub Date : 2024-02-14 DOI: 10.1111/jmi.13274

Abigail Illand, Pierre Jouchet, Emmanuel Fort, Sandrine Lévêque-Fort

{"title":"Flexible implementation of modulated localisation microscopy based on DMD","authors":"Abigail Illand, Pierre Jouchet, Emmanuel Fort, Sandrine Lévêque-Fort","doi":"10.1111/jmi.13274","DOIUrl":"10.1111/jmi.13274","url":null,"abstract":"Localisation microscopy of individual molecules allows one to bypass the diffraction limit, revealing cellular organisation on a nanometric scale. This method, which relies on spatial analysis of the signal emitted by molecules, is often limited to the observation of biological objects at shallow depths, or with very few aberrations. The introduction of a temporal parameter into the localisation process through a time-modulated excitation was recently proposed to address these limitations. This method, called ModLoc, is demonstrated here with an alternative flexible strategy. In this implementation, to encode the time-modulated excitation a digital micromirror device (DMD) is used in combination with a fast demodulation approach, and provides a twofold enhancement in localisation precision.Layout: Nowadays, we can use an optical microscope to observe how proteins are organised in 3D within a cell at the nanoscale. By carefully controlling the emission of molecules in both space and time, we can overcome the limitations set by the diffraction limit. This allows us to pinpoint the exact location of molecules more precisely. However, the usual spatial analysis method limits observations to shallow depths or causing low distortion of optical waves.To overcome these restrictions, a recent approach introduces a temporal element to the localisation process. This involves changing the illumination over time to enhance the precision of localisation. This method, known as ModLoc, is showcased here using a flexible and alternative strategy. In this setup, a matrix of micrometric mirrors, working together with a fast demodulation optical module, is used to encode and decode the time-modulated information. This combination results in a twofold improvement in localisation precision.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139729845","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}

引用次数: 0

A method for crystallographic mapping of an alpha-beta titanium alloy with nanometre resolution using scanning precession electron diffraction and open-source software libraries 利用扫描前驱电子衍射和开源软件库，以纳米分辨率绘制α-β钛合金晶体图的方法。

IF 1.5 4区工程技术

Journal of microscopy Pub Date : 2024-02-14 DOI: 10.1111/jmi.13275

Ian MacLaren, Enrique Frutos-Myro, Steven Zeltmann, Colin Ophus

{"title":"A method for crystallographic mapping of an alpha-beta titanium alloy with nanometre resolution using scanning precession electron diffraction and open-source software libraries","authors":"Ian MacLaren, Enrique Frutos-Myro, Steven Zeltmann, Colin Ophus","doi":"10.1111/jmi.13275","DOIUrl":"10.1111/jmi.13275","url":null,"abstract":"An approach for the crystallographic mapping of two-phase alloys on the nanoscale using a combination of scanned precession electron diffraction and open-source python libraries is introduced in this paper. This method is demonstrated using the example of a two-phase α/β titanium alloy. The data were recorded using a direct electron detector to collect the patterns, and recently developed algorithms to perform automated indexing and analyse the crystallography from the results. Very high-quality mapping is achieved at a 3 nm step size. The results show the expected Burgers orientation relationships between the α laths and β matrix, as well as the expected misorientations between α laths. A minor issue was found that one area was affected by 180° ambiguities in indexing occur due to this area being aligned too close to a zone axis of the α with twofold projection symmetry (not present in 3D) in the zero-order Laue Zone, and this should be avoided in data acquisition in the future. Nevertheless, this study demonstrates a good workflow for the analysis of nanocrystalline two- or multi-phase materials, which will be of widespread use in analysing two-phase titanium and other systems and how they evolve as a function of thermomechanical treatments.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2024-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13275","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139729843","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}

引用次数: 0

Differential phase contrast (DPC) mapping electric fields: Optimising experimental conditions 差分相衬 (DPC) 映射电场：优化实验条件。

IF 2 4区工程技术

Journal of microscopy Pub Date : 2024-02-14 DOI: 10.1111/jmi.13271

Chen Li, Xiaoke Mu, Maxim Korytov, Ioannis Alexandrou, Eric G. T. Bosch

{"title":"Differential phase contrast (DPC) mapping electric fields: Optimising experimental conditions","authors":"Chen Li, Xiaoke Mu, Maxim Korytov, Ioannis Alexandrou, Eric G. T. Bosch","doi":"10.1111/jmi.13271","DOIUrl":"10.1111/jmi.13271","url":null,"abstract":"DPC in Scanning Transmission Electron Microscopy (STEM) is a valuable method for mapping the electric fields in semiconductor materials. However, optimising the experimental conditions can be challenging. In this paper, we test and compare critical experimental parameters, including the convergence angle, camera length, acceleration voltage, sample configuration, and orientation using a four-quadrant segmented detector and a Si specimen containing layers of different As concentrations. The DPC measurements show a roughly linear correlation with the estimated electric fields, until the field gets close to the detection limitation, which is ∼0.5 mV/nm with a sample thickness of ∼145 nm. These results can help inform which technique to use for different user cases: When the electric field at a planar junction is above ∼0.5 mV/nm, DPC with a segmented detector is practical for electric field mapping. With a planar junction, the DPC signal-to-noise ratio can be increased by increasing the specimen thickness. However, for semiconductor devices with electric fields smaller than ∼0.5 mV/nm, or for devices containing curved junctions, DPC is unreliable and techniques with higher sensitivity will need to be explored, such as 4D STEM using a pixelated detector.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139729844","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}

引用次数: 0

On the pixel selection criterion for the calculation of the Pearson's correlation coefficient in fluorescence microscopy. 关于荧光显微镜中计算皮尔逊相关系数的像素选择标准。

IF 2 4区工程技术

Journal of microscopy Pub Date : 2024-02-13 DOI: 10.1111/jmi.13273

Sergio G Lopez, Sebastian Samwald, Sally Jones, Christine Faulkner

{"title":"On the pixel selection criterion for the calculation of the Pearson's correlation coefficient in fluorescence microscopy.","authors":"Sergio G Lopez, Sebastian Samwald, Sally Jones, Christine Faulkner","doi":"10.1111/jmi.13273","DOIUrl":"https://doi.org/10.1111/jmi.13273","url":null,"abstract":"Colocalisation microscopy analysis provides an intuitive and straightforward way of determining if two biomolecules occupy the same diffraction-limited volume. A popular colocalisation coefficient, the Pearson's correlation coefficient (PCC), can be calculated using different pixel selection criteria: PCCALL includes all image pixels, PCCOR only pixels exceeding the intensity thresholds for either one of the detection channels, and PCCAND only pixels exceeding the intensity thresholds for both detection channels. Our results show that PCCALL depends on the foreground to background ratio, producing values influenced by factors unrelated to biomolecular association. PCCAND focuses on areas with the highest intensities in both channels, which allows it to detect low levels of colocalisation, but makes it inappropriate for evaluating spatial cooccurrence between the signals. PCCOR produces values influenced both by signal proportionality and spatial cooccurrence but can sometimes overemphasise the lack of the latter. Overall, PCCAND excels at detecting low levels of colocalisation, PCCOR provides a balanced quantification of signal proportionality and spatial coincidence, and PCCALL risks misinterpretation yet avoids segmentation challenges. Awareness of their distinct properties should inform their appropriate application with the aim of accurately representing the underlying biology.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139722975","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}

引用次数: 0

Mitophagy in plants: Emerging regulators of mitochondrial targeting for selective autophagy. 植物的线粒体吞噬：线粒体靶向选择性自噬的新调节器

IF 2 4区工程技术

Journal of microscopy Pub Date : 2024-01-31 DOI: 10.1111/jmi.13267

Patrick J Duckney, Pengwei Wang, Patrick J Hussey

{"title":"Mitophagy in plants: Emerging regulators of mitochondrial targeting for selective autophagy.","authors":"Patrick J Duckney, Pengwei Wang, Patrick J Hussey","doi":"10.1111/jmi.13267","DOIUrl":"https://doi.org/10.1111/jmi.13267","url":null,"abstract":"The degradation and turnover of mitochondria is fundamental to Eukaryotes and is a key homeostatic mechanism for maintaining functional mitochondrial populations. Autophagy is an important pathway by which mitochondria are degraded, involving their sequestration into membrane-bound autophagosomes and targeting to lytic endosomal compartments (the lysosome in animals, the vacuole in plants and yeast). Selective targeting of mitochondria for autophagy, also known as mitophagy, distinguishes mitochondria from other cell components for degradation and is necessary for the regulation of mitochondria-specific cell processes. In mammals and yeast, mitophagy has been well characterised and is regulated by numerous pathways with diverse and important functions in the regulation of cell homeostasis, metabolism and responses to specific stresses. In contrast, we are only just beginning to understand the importance and functions of mitophagy in plants, chiefly as the proteins that target mitochondria for autophagy in plants are only recently emerging. Here, we discuss the current progress of our understanding of mitophagy in plants, the importance of mitophagy for plant life and the regulatory autophagy proteins involved in mitochondrial degradation. In particular, we will discuss the recent emergence of mitophagy receptor proteins that selectively target mitochondria for autophagy, and discuss the missing links in our knowledge of mitophagy-regulatory proteins in plants compared to animals and yeast.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139650918","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}

引用次数: 0

Multimodal optical mesoscopy reveals the quantity and spatial distribution of Gram-positive biofilms in ex vivo tonsils 多模态光学介孔镜揭示了体外扁桃体中革兰氏阳性生物膜的数量和空间分布。

IF 1.5 4区工程技术

Journal of microscopy Pub Date : 2024-01-31 DOI: 10.1111/jmi.13266

Megan Clapperton, Tash Kunanandam, Catalina D. Florea, Catriona M. Douglas, Gail McConnell

{"title":"Multimodal optical mesoscopy reveals the quantity and spatial distribution of Gram-positive biofilms in ex vivo tonsils","authors":"Megan Clapperton, Tash Kunanandam, Catalina D. Florea, Catriona M. Douglas, Gail McConnell","doi":"10.1111/jmi.13266","DOIUrl":"10.1111/jmi.13266","url":null,"abstract":"Biofilms are known to be present in tonsils, but little is known about their spatial location and size distribution throughout the tonsil. Studies of the location and distribution of biofilms in tonsil specimens have thus far been limited to either high-magnification methods such as electron microscopy, which enables high-resolution imaging but only from a tiny tissue volume, or lower magnification techniques such as light microscopy, which allow imaging of larger specimens but with poor spatial resolution. To overcome these limitations, we report the use of multimodal optical mesoscopy to visualise and quantify the number and spatial distribution of Gram-positive biofilms in fresh, excised paediatric tonsils. This methodology supports simultaneous imaging of both the tonsil host and biofilms in whole mounts of tissue up to 5 mm × 5 mm × 3 mm with subcellular resolution throughout. A quantitative assessment of 36 tonsil specimens revealed no statistically significant difference between biofilm presence on the tonsil surface and the interior of the tonsil. This new quantitative mesoscale imaging approach may prove useful in understanding the role of biofilms in tonsillar diseases and other infections.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13266","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139650919","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}

引用次数: 0

An automated slide scanning system for membrane filter imaging in diagnosis of urogenital schistosomiasis 用于诊断尿路血吸虫病的膜过滤成像自动玻片扫描系统。

IF 2 4区工程技术

Journal of microscopy Pub Date : 2024-01-30 DOI: 10.1111/jmi.13269

Prosper Oyibo, Tope Agbana, Lisette van Lieshout, Wellington Oyibo, Jan-Carel Diehl, Gleb Vdovine

{"title":"An automated slide scanning system for membrane filter imaging in diagnosis of urogenital schistosomiasis","authors":"Prosper Oyibo, Tope Agbana, Lisette van Lieshout, Wellington Oyibo, Jan-Carel Diehl, Gleb Vdovine","doi":"10.1111/jmi.13269","DOIUrl":"10.1111/jmi.13269","url":null,"abstract":"Traditionally, automated slide scanning involves capturing a rectangular grid of field-of-view (FoV) images which can be stitched together to create whole slide images, while the autofocusing algorithm captures a focal stack of images to determine the best in-focus image. However, these methods can be time-consuming due to the need for X-, Y- and Z-axis movements of the digital microscope while capturing multiple FoV images. In this paper, we propose a solution to minimise these redundancies by presenting an optimal procedure for automated slide scanning of circular membrane filters on a glass slide. We achieve this by following an optimal path in the sample plane, ensuring that only FoVs overlapping the filter membrane are captured. To capture the best in-focus FoV image, we utilise a hill-climbing approach that tracks the peak of the mean of Gaussian gradient of the captured FoVs images along the Z-axis. We implemented this procedure to optimise the efficiency of the Schistoscope, an automated digital microscope developed to diagnose urogenital schistosomiasis by imaging Schistosoma haematobium eggs on 13 or 25 mm membrane filters. Our improved method reduces the automated slide scanning time by 63.18% and 72.52% for the respective filter sizes. This advancement greatly supports the practicality of the Schistoscope in large-scale schistosomiasis monitoring and evaluation programs in endemic regions. This will save time, resources and also accelerate generation of data that is critical in achieving the targets for schistosomiasis elimination.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13269","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139642366","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}

引用次数: 0

Preface to the special issue on Microscopy of Semiconducting Materials 2023 2023 年半导体材料显微学特刊序言。

IF 2 4区工程技术

Journal of microscopy Pub Date : 2024-01-28 DOI: 10.1111/jmi.13265

Thomas Walther, Rachel A Oliver

引用次数: 0

A rapid freezing method to determine tissue layer thickness in drought-stressed leaves. 快速冷冻法测定干旱胁迫叶片的组织层厚度。

IF 2 4区工程技术

Journal of microscopy Pub Date : 2024-01-28 DOI: 10.1111/jmi.13272

Maryam Alsadat Zekri, Carina Leimhofer, Nicole Drexler, Ingeborg Lang

{"title":"A rapid freezing method to determine tissue layer thickness in drought-stressed leaves.","authors":"Maryam Alsadat Zekri, Carina Leimhofer, Nicole Drexler, Ingeborg Lang","doi":"10.1111/jmi.13272","DOIUrl":"https://doi.org/10.1111/jmi.13272","url":null,"abstract":"Plants have been affected by water stress ever since they settled on dry land. In severe and persisting drought, plant leaves are wilting. However, a documentation at the anatomical level of the minute changes that occur before wilting is challenging. On the other hand, understanding the anatomical alteration in plant leaves with respect to water stress provides a stronger basis to study molecular and submolecular processes through which plants enhance drought tolerance. In this work, we applied an affordable method to visualise mesophyll layers of Arabidopsis thaliana cell lines without preparation steps that would alter the volume of the cells. We rapidly plunge-froze the leaves in liquid nitrogen, cut them while in the N2 bath, and immediately imaged the mesophyll cross sections in a scanning electron microscope. We applied a reduction of watering from 60 to 40 to 20 mL per day and investigated two time points, 7 and 12 days, respectively. Interestingly, the overall thickness of leaves increased in water stress conditions. Our results showed that the palisade and spongy layers behaved differently under varying watering regimes. Moreover, the results showed that this method can be used to image leaf sections after drought stress without the risk of artefacts or swelling caused by contact to liquids as during chemical fixation.","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570742","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}

引用次数: 0

Artificial intelligence: Transforming the role of technical expertise in Microscopy field 人工智能：改变显微镜领域专业技术的角色。

IF 2 4区工程技术

Journal of microscopy Pub Date : 2024-01-24 DOI: 10.1111/jmi.13268

Bhagyashri Patil-Takbhate

引用次数: 0