Robert S Matos, Erveton P Pinto, Marcelo A Pires, Glenda Q Ramos, Ştefan Ţălu, Lucas S Lima, Henrique D da Fonseca Filho
{"title":"Evaluating the roughness dynamics of kefir biofilms grown on Amazon cupuaçu juice: a monofractal and multifractal approach.","authors":"Robert S Matos, Erveton P Pinto, Marcelo A Pires, Glenda Q Ramos, Ştefan Ţălu, Lucas S Lima, Henrique D da Fonseca Filho","doi":"10.1093/jmicro/dfad040","DOIUrl":"10.1093/jmicro/dfad040","url":null,"abstract":"<p><p>We conducted a comprehensive analysis of the surface microtexture of kefir biofilms grown on Theobroma grandiflorum Shum (cupuaçu) juice using atomic force microscopy. Our goal was to investigate the unique monofractal and multifractal spatial patterns of these biofilms to complement the existing limited literature. The biofilms were prepared dispersing four different concentrations of kefir grains in cupuaçu juice. Our morphological analysis showed that the surface of the obtained biofilms is essentially formed by the presence of cupuaçu fibers and microorganisms like lactobacilli and yeast. The topographic height-based parameter analysis reveals that there is a dependence between surface roughness and the concentration of kefir grains used. The strongly anisotropic well-centralized topographical height distribution of the biofilms also exhibited a quasi-symmetrical and platykurtic pattern. The biofilms exhibit comparable levels of spatial complexity, surface percolation and surface homogeneity, which can be attributed to their similar topographic uniformity. This aspect was further supported by the presence of similar multifractality in the biofilms, suggesting that despite their varying topographic roughness, their vertical growth dynamics follow a similar pattern. Our findings demonstrate that the surface roughness of kefir biofilms cultivated on cupuaçu juice is influenced by the concentration of kefir grains in the precursor solution. However, this dependence follows a consistent pattern across different concentrations. Graphical Abstract.</p>","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":"55-65"},"PeriodicalIF":0.0,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9937529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Prediction of secondary electron yield for metal materials using deep learning.","authors":"Masahiro Kusumi, Bunta Inoue, Yoshihiko Hirai, Masaaki Yasuda","doi":"10.1093/jmicro/dfad034","DOIUrl":"10.1093/jmicro/dfad034","url":null,"abstract":"<p><p>This article describes a neural network system for predicting the secondary electron yield of metallic materials. For bulk metals, experimental values are used as training data. Due to the strong correlation between the secondary electron yield and the work function, deep learning predicts the secondary electron yield with relatively high accuracy even with a small amount of training data. Our approach demonstrates the importance of the work function in predicting the secondary electron yield. For the secondary electron yield of thin metal films on metal substrates, deep learning predictions are generated using training data obtained by Monte Carlo simulations. The accuracy of the secondary yield predictions of thin films on substrates could be improved by adding experimental values of bulk metals to the training data.</p>","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":"31-36"},"PeriodicalIF":0.0,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9601340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Enhancing performance of electron holography with mathematical and machine learning-based denoising techniques.","authors":"Satoshi Anada, Yuki Nomura, Kazuo Yamamoto","doi":"10.1093/jmicro/dfad037","DOIUrl":"10.1093/jmicro/dfad037","url":null,"abstract":"<p><p>Electron holography is a useful tool for analyzing functional properties, such as electromagnetic fields and strains of materials and devices. The performance of electron holography is limited by the 'shot noise' inherent in electron micrographs (holograms), which are composed of a finite number of electrons. A promising approach for addressing this issue is to use mathematical and machine learning-based image-processing techniques for hologram denoising. With the advancement of information science, denoising methods have become capable of extracting signals that are completely buried in noise, and they are being applied to electron microscopy, including electron holography. However, these advanced denoising methods are complex and have many parameters to be tuned; therefore, it is necessary to understand their principles in depth and use them carefully. Herein, we present an overview of the principles and usage of sparse coding, the wavelet hidden Markov model and tensor decomposition, which have been applied to electron holography. We also present evaluation results for the denoising performance of these methods obtained through their application to simulated and experimentally recorded holograms. Our analysis, review and comparison of the methods clarify the impact of denoising on electron holography research.</p>","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":"461-484"},"PeriodicalIF":0.0,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10143776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aadil Sheikh, Bernd Zechmann, Christie M Sayes, Joseph H Taube, K Leigh Greathouse
{"title":"A preparation of bacterial outer membrane with osmium tetroxide and uranyl acetate co-stain enables improved structural determination by transmission electron microscopy.","authors":"Aadil Sheikh, Bernd Zechmann, Christie M Sayes, Joseph H Taube, K Leigh Greathouse","doi":"10.1093/jmicro/dfad027","DOIUrl":"10.1093/jmicro/dfad027","url":null,"abstract":"<p><p>Biological nanoparticles, such as bacterial outer membrane vesicles (OMVs), are routinely characterized through transmission electron microscopy (TEM). In this study, we report a novel method to prepare OMVs for TEM imaging. To preserve vesicular shape and structure, we developed a dual fixation protocol involving osmium tetroxide incubation prior to negative staining with uranyl acetate. Combining osmium tetroxide with uranyl acetate resulted in preservation of sub-50 nm vesicles and improved morphological stability, enhancing characterization of lipid-based nanoparticles by TEM.</p>","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":"515-519"},"PeriodicalIF":0.0,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10673695/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9765936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A novel embedding composition for the evaluation of the internal structure of carbon materials using electron microscopy.","authors":"Tsukaho Yahagi","doi":"10.1093/jmicro/dfad020","DOIUrl":"10.1093/jmicro/dfad020","url":null,"abstract":"<p><p>The image contrast obtained in electron microscopy depends on the atomic number of the sample. Therefore, obtaining a clear contrast is challenging when samples composed of light elements (carbon materials and polymers) are embedded in the resin. Herein, a newly developed embedding composition exhibiting low viscosity and high electron density is reported, which can be solidified using physical or chemical methods. When used for carbon materials, this embedding composition allows clear microscopic observation with higher contrast compared to conventional resin embedding. Furthermore, details of the observation of samples such as graphite and carbon black using this embedding composition are reported.</p>","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":"511-514"},"PeriodicalIF":0.0,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9140890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yevheniy Pivak, Junbeom Park, Shibabrata Basak, Rüdiger-Albert Eichel, Anne Beker, Alejandro Rozene, Héctor Hugo Pérez Garza, Hongyu Sun
{"title":"High-resolution and analytical electron microscopy in a liquid flow cell via gas purging.","authors":"Yevheniy Pivak, Junbeom Park, Shibabrata Basak, Rüdiger-Albert Eichel, Anne Beker, Alejandro Rozene, Héctor Hugo Pérez Garza, Hongyu Sun","doi":"10.1093/jmicro/dfad023","DOIUrl":"10.1093/jmicro/dfad023","url":null,"abstract":"<p><p>Liquid-phase transmission electron microscopy (LPTEM) technique has been used to perform a wide range of in situ and operando studies. While most studies are based on the sample contrast change in the liquid, acquiring high qualitative results in the native liquid environment still poses a challenge. Herein, we present a novel and facile method to perform high-resolution and analytical electron microscopy studies in a liquid flow cell. This technique is based on removing the liquid from the observation area by a flow of gas. It is expected that the proposed approach can find broad applications in LPTEM studies.</p>","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":"520-524"},"PeriodicalIF":0.0,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9641816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Salma Khanam, Takayuki Funatsu, Koji Tanaka, Yasuko Kaneko
{"title":"Using a novel CLEM system to localize lipid droplets and membranes in desiccated embryonic axis cells of soybean seeds.","authors":"Salma Khanam, Takayuki Funatsu, Koji Tanaka, Yasuko Kaneko","doi":"10.1093/jmicro/dfad017","DOIUrl":"10.1093/jmicro/dfad017","url":null,"abstract":"<p><p>Lipid droplets and membranes in radicle cells from desiccated embryonic axes of soybean (Glycine max) seeds were examined by a recently developed correlative light and electron microscopy system, which has been designed to facilitate the observation of identical locations using an upright reflected light microscope and compact SEM successively with minimum time lapse. Lipids are major components of membranes and are also stored in numerous lipid droplets lining plasma membranes in many seed cells. Fluorescently stained lipid droplets and membranes in the desiccated radicle cells were mainly located along the surface of shrunk protoplasm and around presumptive protein bodies, which will turn into vacuoles and increase their volume for radicle protrusion. Co-localization of lipid droplets and membranes suggests the presence of a membrane protection mechanism during desiccation and rehydration processes that ensures prompt elongation of radicle cells during germination.</p>","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":"506-510"},"PeriodicalIF":0.0,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9332069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Low-dose measurement of electric potential distribution in organic light-emitting diode by phase-shifting electron holography with 3D tensor decomposition.","authors":"Yusei Sasaki, Kazuo Yamamoto, Satoshi Anada, Noriyuki Yoshimoto","doi":"10.1093/jmicro/dfad019","DOIUrl":"10.1093/jmicro/dfad019","url":null,"abstract":"<p><p>To improve the performance of organic light-emitting diodes (OLEDs), it is essential to understand and control the electric potential in the organic semiconductor layers. Electron holography (EH) is a powerful technique for visualizing the potential distribution with a transmission electron microscope. However, it has a serious issue that high-energy electrons may damage the organic layers, meaning that a low-dose EH is required. Here, we used a machine learning technique, three-dimensional (3D) tensor decomposition, to denoise electron interference patterns (holograms) of bilayer OLEDs composed of N,N'-di-[(1-naphthyl)-N,N'-diphenyl]-(1,1'-biphenyl)-4,4'-diamine (α-NPD) and tris-(8-hydroxyquinoline)aluminum (Alq3), acquired under a low-dose rate of 130 e- nm-2 s-1. The effect of denoising on the phase images reconstructed from the holograms was evaluated in terms of both the phase measurement error and the peak signal-to-noise ratio. We achieved a precision equivalent to that of a conventional measurement that had an exposure time 60 times longer. The electric field within the Alq3 layer decreased as the cumulative dose increased, which indicates that the Alq3 layer was degraded by the electron irradiation. On the basis of the degradation of the electric field, we concluded that the tolerance dose without damaging the OLED sample is about 1.7 × 105 e- nm-2, which is about 0.6 times that of the conventional EH. The combination of EH and 3D tensor decomposition denoising is capable of making a time series measurement of an OLED sample without any effect from the electron irradiation.</p>","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":"485-493"},"PeriodicalIF":0.0,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10783859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"In situ pulsed electrical biasing TEM observation of AA7075.","authors":"Tyler J Grimm, Laine Mears","doi":"10.1093/jmicro/dfad025","DOIUrl":"10.1093/jmicro/dfad025","url":null,"abstract":"<p><p>Electrically assisted heat treatment is the process of applying an electric current to a sample during heat treatment. Literature has generally shown there to be a difference in the resulting effects of direct current (DC) current and highly transient current (i.e. electropulsing). However, these differences are poorly characterized. In situ transmission electron microscopy (TEM) observation of an AA7075 sample while DC and pulsed current were passed through it was performed herein to explore the effects of an electric current on precipitate development. Numerical simulation results indicate that the thermal response of the samples was very rapid, causing the sample to reach steady-state temperatures almost instantly. There does not appear to be any significant difference between the results of pulsed current application and DC current. Additionally, the failure mechanism of an electrical biasing TEM sample is explored.</p>","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":"494-505"},"PeriodicalIF":0.0,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9400143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Analyzing the synchronism of stacking-fault formation in side-by-side SiC nanowire pairs using the Levenshtein distance: stochastic versus deterministic processes.","authors":"Fuka Moriuchi, Hideo Kohno","doi":"10.1093/jmicro/dfac073","DOIUrl":"10.1093/jmicro/dfac073","url":null,"abstract":"<p><p>Pairs of silicon carbide nanowires were grown side by side synchronously from the same metal catalyst nanoparticles. The stacking sequences of each pair were read by high-resolution transmission electron microscopy, and the similarity of each stacking sequence was measured using the Levenshtein distance. No synchronism was detected in the pairs of stacking sequences, and the results indicated that the formation of stacking faults in silicon carbide nanowires was not deterministic, but purely stochastic.</p>","PeriodicalId":74193,"journal":{"name":"Microscopy (Oxford, England)","volume":" ","pages":"395-398"},"PeriodicalIF":0.0,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10444312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}