Journal of microscopy最新文献

{"title":"AutoSAFT: Autofocusing for extended depth of imaging in scanning acoustic microscopy","authors":"M Sarim Ameed Khan,&nbsp;Shivam Ojha,&nbsp;Shubham Kumar Gupta,&nbsp;Amit Shelke,&nbsp;Azeem Ahmad,&nbsp;Frank Melandsø,&nbsp;Anowarul Habib","doi":"10.1111/jmi.13399","DOIUrl":"10.1111/jmi.13399","url":null,"abstract":"<p>In the scanning acoustic microscopy (SAM) imaging, it is essential to address the diminished lateral resolution in the out-of-focus region, as image quality correlates with the ultrasound propagation distance either above or below the focal plane. To focus the scanned image, a refocusing technique called synthetic aperture focusing technique (SAFT) is widely used, which improves the resolution by extending the depth of focus manually. In SAM, refocusing the image accurately is challenging without prior defocusing information. This paper introduces AutoSAFT, an automated version of SAFT. It employs the reference-less image-quality index (IQI) called Blind/Referenceless Image Spatial Quality Evaluator (BRISQUE) score to evaluate and optimise the defocusing distance automatically. The focused images were qualitatively analysed using metrics such as structural similarity index matrix (SSIM) and peak signal-to-noise ratio (PSNR). The combined qualitative and quantitative analysis demonstrates that the AutoSAFT technique is the most suitable method for the automatic focusing of acoustic imaging from the SAM. The proposed AutoSAFT opens a new avenue in photoacoustic image focusing methodologies.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"298 3","pages":"283-292"},"PeriodicalIF":1.5,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13399","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143502059","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 3D-printed optical microscope for low-cost histological imaging","authors":"Jay Christopher,&nbsp;Rebecca Craig,&nbsp;Rebecca E. McHugh,&nbsp;Andrew J. Roe,&nbsp;Ralf Bauer,&nbsp;Brian Patton,&nbsp;Gail McConnell,&nbsp;Liam M. Rooney","doi":"10.1111/jmi.13398","DOIUrl":"10.1111/jmi.13398","url":null,"abstract":"<p>We present the manufacture and characterisation of a 3D-printed, low-cost optical microscope using both a 3D-printed chassis and 3D-printed illumination and imaging optics. The required commercial components, consisting of a basic camera for image acquisition and light emitting diode controlled by a Raspberry Pi for illumination, are integrated into the 3D-printed microscope with the full design shown for ease of replication. Our 3D-printed microscope uses a single 3D-printed objective lens with a 2.9× magnification and a numerical aperture of 0.07. To benchmark the imaging performance of the system, we used standard test targets and histological specimens, namely, a Giemsa-stained blood smear sample and a thin section of mouse kidney stained with haemotoxylin and eosin. We demonstrated that subcellular resolution was obtained, and we corroborated this by imaging individual red blood cells and intricate anatomical details of the stained mouse kidney section. All of this was achieved using entirely 3D-printed hardware and optics, at a fraction of the cost of a commercial bright-field microscope, while presenting remarkable potential for customisation and increased accessibility for diagnostic imaging applications.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"298 3","pages":"274-282"},"PeriodicalIF":1.5,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13398","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492417","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":"Quantitative analysis of human umbilical vein endothelial cell morphology and tubulogenesis.","authors":"Viviane Mignone, Maria Augusta Arruda, Laura Kilpatrick, Benjamin Moore, Jeanette Woolard, Stephen Hill, Joëlle Goulding","doi":"10.1111/jmi.13397","DOIUrl":"https://doi.org/10.1111/jmi.13397","url":null,"abstract":"<p><p>Primary human umbilical vein endothelial cells can grow as both a monolayer in culture and also as a capillary-like network making them an ideal model system in order to study vascular remodelling. Image-based analysis can allow assessment of cell morphology and motility but is dependent on accurate cell segmentation which requires high-contrast images not normally achievable without fluorescent markers. Here, ptychography is employed as a label-free image-based modality in order to extract quantitative metrics of morphology and tubulogenesis from cultured HUVECs over time in an automated multiwell assay. Phase-specific parameters of dry mass, optical thickness and sphericity were extracted and assessed alongside other metrics of cell number and shape. Tubulogenesis could be captured dynamically without any imaging artefacts from use of a basement membrane matrix and metrics of tube number, growth and branching exported alongside morphology metrics at early time-points. Utilising ptychography-based image analysis, all VEGF₁₆₅a isoforms studied, elicited a concentration-dependent effect on cell elongation and survival within a HUVEC monolayer. Pharmacologically relevant parameters of potency (EC₅₀) and efficacy were derived, exemplifying this label-free approach for the multiparameter and multiwell quantitative study of vascular remodelling in physiologically relevant cells at 37°C.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468341","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":"Uncertainties in interfacial excess calculations from atom probe tomography data","authors":"Levi Tegg,&nbsp;Julie M. Cairney","doi":"10.1111/jmi.13392","DOIUrl":"10.1111/jmi.13392","url":null,"abstract":"<p>Atom probe tomography can be used to measure the excess of solute chemical species at internal interfaces, but common protocols do not usually consider the compositional uncertainty of the (usually dilute) solute. Here, general models are derived for the composition profile of a solute segregated to the interface between two grains or phases. This model is fit to experimental data, with the cumulative compositional uncertainty included in the calculation of the interfacial excess. It is shown that the relative uncertainty in the interfacial excess can be large for dilute solutes, even when segregation is obvious in the concentration profile. Different methods for estimating the extent of the boundary provide different estimates for the interfacial excess and its uncertainty. Some strategies are provided for the minimisation of uncertainties in typical data, though ultimately, a typical calculation will be limited by compositional uncertainty arising from the relatively few solute counts in the region-of-interest.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"298 3","pages":"262-273"},"PeriodicalIF":1.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13392","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468403","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":"Modulation of host cell membrane biophysics dynamics by Neospora caninum: A study using LAURDAN fluorescence with hyperspectral imaging and phasor analysis.","authors":"Marcela Díaz, Carlos Robello, Andrés Cabrera, Leonel Malacrida","doi":"10.1111/jmi.13395","DOIUrl":"https://doi.org/10.1111/jmi.13395","url":null,"abstract":"<p><p>Neospora caninum is known to manipulate host cell organelles and recruit lipids for its survival. However, the impact of this lipid redistribution on host cell membranes remains poorly understood. This study used LAURDAN fluorescence, hyperspectral imaging, and phasor plot analysis to investigate how N. caninum modifies membrane order in Vero cells. The results revealed a significant decrease in host cell plasma and internal membrane order upon infection, suggesting that cholesterol is redistributed from the host plasma membrane to the parasitophorous vacuoles. To mimic cholesterol depletion, uninfected cells were treated with methyl-β-cyclodextrin (MBCD), which increased membrane fluidity. Conversely, replenishing infected cells with cholesterol-loaded MBCD restored membrane fluidity to levels lower than control cells, indicating cholesterol enrichment. These findings provide novel insights into how N. caninum modulates host cell membrane dynamics through lipid manipulation, potentially aiding its intracellular survival.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457835","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":"Investigation of sedimentary rocks and grains in the round: Micron-scale SEM-BEX 360° and 3D imaging","authors":"Jim Buckman","doi":"10.1111/jmi.13389","DOIUrl":"10.1111/jmi.13389","url":null,"abstract":"<p>The aim of the current paper is to demonstrate the use of a novel prototype horizontal rotation stage, within a scanning electron microscope (SEM). Here we utilise sedimentary rock chips and grains, with images collected every 10 ° of rotation, to produce a continuous overlapping field of view 360° montage. The same procedure can also be used to collect elemental X-ray maps. The collected images and maps can be simply combined into an image stack and saved as a movie format of the rotating specimen through 360°. More significantly, individual images and elemental maps can be reconstructed using photogrammetry imaging software, producing three-dimensional (3D) models with mesh worked surfaces and rendered texture (colour or greyscale) based on SEM image and X-ray data. This produces photorealistic smoothly transitioning movies with 360° fields of view around each object and can also be saved for stereo-viewing using a virtual reality (VR) headset. This new technique generates highly detailed information on the 3D structural and compositional relationships between components at the submicron to millimetre scale. The technique has widespread applications, including imaging other geological materials, biological mineralised tests and material science specimens such as metals, ceramics and building materials.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"298 3","pages":"254-261"},"PeriodicalIF":1.5,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13389","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143399324","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":"TOC - Issue Information","authors":"","doi":"10.1111/jmi.13324","DOIUrl":"https://doi.org/10.1111/jmi.13324","url":null,"abstract":"","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"297 3","pages":"253-254"},"PeriodicalIF":1.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13324","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143380144","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":"TUNA-EBSD-CL correlative multi-microscopy study, on the example of Cu(In,Ga)S2 solar cell absorber","authors":"Yucheng Hu,&nbsp;Gunnar Kusch,&nbsp;Damilola Adeleye,&nbsp;Susanne Siebentritt,&nbsp;Rachel Oliver","doi":"10.1111/jmi.13393","DOIUrl":"10.1111/jmi.13393","url":null,"abstract":"<p>Multi-microscopy offers significant benefits to the understanding of complex materials behaviour by providing complementary information from different properties. However, some characterisations may strongly influence other measurements in the same workflow. To acquire reliable and valid datasets, optimising multi-microscopy procedure is necessary. In present work, we studied the influence of the measurement order on the quality of multi-microscopy datasets. Multi-microscopy incorporating tunnelling current AFM (TUNA), electron backscatter diffraction (EBSD), and cathodoluminescence (CL) on a polycrystalline solar cell absorber, Cu(In,Ga)S₂ (CIGS), is used as an example. The investigation revealed potential characterisation-induced contaminations, such as surface oxidation and hydrocarbon layer coating, of the sample surface. Their subsequent influence on the measurement results of following correlation techniques was examined. To optimise the dataset quality, multi-microscopy should be carried out in TUNA-EBSD-CL order, from the most to the least surface sensitive techniques. With the optimised multi-microscopy measurement order on a CIGS absorber, we directly correlated the local changes in electrical and opto-electronic properties with the microstructure of grain boundaries (GBs). The described methodology may also provide insightful concepts for applying other AFM-SEM-based multi-microscopy on different semiconductor materials.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"298 1","pages":"106-117"},"PeriodicalIF":1.5,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13393","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080378","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":"Native state structural and chemical characterisation of Pickering emulsions: A cryo-electron microscopy study","authors":"Dario Luis Fernandez Ainaga,&nbsp;Teresa Roncal-Herrero,&nbsp;Martha Ilett,&nbsp;Zabeada Aslam,&nbsp;Cheng Cheng,&nbsp;James P. Hitchcock,&nbsp;Olivier J. Cayre,&nbsp;Nicole Hondow","doi":"10.1111/jmi.13391","DOIUrl":"10.1111/jmi.13391","url":null,"abstract":"<p>Transmission electron microscopy can be used for the characterisation of a wide range of thin specimens, but soft matter and aqueous samples such as gels, nanoparticle dispersions, and emulsions will dry out and collapse under the microscope vacuum, therefore losing information on their native state and ultimately limiting the understanding of the sample.</p><p>This study examines commonly used techniques in transmission electron microscopy when applied to the characterisation of cryogenically frozen Pickering emulsion samples. Oil-in-water Pickering emulsions stabilised by 3 to 5 nm platinum nanoparticles were cryogenically frozen by plunge-freezing into liquid ethane to retain the native structure of the system without inducing crystallisation of the droplet oil cores.</p><p>A comparison between the droplet morphology following different sample preparation methods has confirmed the effectiveness of using plunge-freezing to prepare these samples. Scanning transmission electron microscopy imaging showed that dry droplets collapse under the microscope vacuum, changing their shape and size (average apparent diameter: ∼342 nm) compared to frozen samples (average diameter: ∼183 nm). Cryogenic electron tomography was used to collect additional information of the 3D shape and size of the emulsion droplets, and the position of the stabilising nanoparticles relative to the droplet surface. Cryogenic energy dispersive X-ray and electron energy loss spectroscopy were used to successfully obtain elemental data and generate elemental maps to identify the stabilising nanoparticles and the oil phase. Elemental maps generated from spectral data were used in conjunction with electron tomography to obtain 3D information of the oil phase in the emulsion droplets.</p><p>Beam-induced damage to the ice was the largest limiting factor to the sample characterisation, limiting the effective imaging resolution and signal-to-noise ratio, though careful consideration of the imaging parameters used allowed for the characterisation of the samples presented in this study. Ultimately this study shows that cryo-methods are effective for the representative characterisation of Pickering emulsions.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"298 1","pages":"92-105"},"PeriodicalIF":1.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13391","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066063","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":"Automated Euler number of the alveolar capillary network based on deep learning segmentation with verification by stereological methods","authors":"Julia Schmidt,&nbsp;Jonas Labode,&nbsp;Christoph Wrede,&nbsp;Yannick Regin,&nbsp;Jaan Toelen,&nbsp;Christian Mühlfeld","doi":"10.1111/jmi.13390","DOIUrl":"10.1111/jmi.13390","url":null,"abstract":"<p>Diseases like bronchopulmonary dysplasia (BPD) affect the development of the pulmonary vasculature, including the alveolar capillary network (ACN). Since pulmonary development is highly dependent on angiogenesis and microvascular maturation, ACN investigations are essential. Therefore, efficient methods are needed for quantitative comparative studies. Here, the suitability of deep learning (DL) for processing serial block-face scanning electron microscopic (SBF-SEM) data by generating ACN segmentations, 3D reconstructions and performing automated quantitative analyses based on them, was tested. Since previous studies revealed inefficient ACN segmentation as the limiting factor in the overall workflow, a 2D DL-based approach was used with existing data, aiming at the reduction of necessary manual interaction. Automated quantitative analyses based on completed segmentations were performed subsequently. The results were compared to stereological estimations, assessing segmentation quality and result reliability. It was shown that the DL-based approach was suitable for generating segmentations on SBF-SEM data. This approach generated more complete initial ACN segmentations than an established method, despite the limited amount of available training data and the use of a 2D rather than a 3D approach. The quality of the completed ACN segmentations was assessed as sufficient. Furthermore, quantitative analyses delivered reliable results about the ACN architecture, automatically obtained contrary to manual stereological approaches. This study demonstrated that ACN segmentation is still the part of the overall workflow that requires improvement regarding the reduction of manual interaction to benefit from available automated software tools. Nevertheless, the results indicated that it could be advantageous taking further efforts to implement a 3D DL-based segmentation approach. As the amount of analysed data was limited, this study was not conducted to obtain representative data about BPD-induced ACN alterations, but to highlight next steps towards a fully automated segmentation and evaluation workflow, enabling larger sample sizes and representative studies.</p>","PeriodicalId":16484,"journal":{"name":"Journal of microscopy","volume":"298 1","pages":"74-91"},"PeriodicalIF":1.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jmi.13390","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066044","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}