Applied Microscopy最新文献

{"title":"Advanced atomic force microscopy-based techniques for nanoscale characterization of switching devices for emerging neuromorphic applications","authors":"Young-Min Kim,&nbsp;Jihye Lee,&nbsp;Deok-Jin Jeon,&nbsp;Si-Eun Oh,&nbsp;Jong-Souk Yeo","doi":"10.1186/s42649-021-00056-9","DOIUrl":"https://doi.org/10.1186/s42649-021-00056-9","url":null,"abstract":"<p>Neuromorphic systems require integrated structures with high-density memory and selector devices to avoid interference and recognition errors between neighboring memory cells. To improve the performance of a selector device, it is important to understand the characteristics of the switching process. As changes by switching cycle occur at local nanoscale areas, a high-resolution analysis method is needed to investigate this phenomenon. Atomic force microscopy (AFM) is used to analyze the local changes because it offers nanoscale detection with high-resolution capabilities. This review introduces various types of AFM such as conductive AFM (C-AFM), electrostatic force microscopy (EFM), and Kelvin probe force microscopy (KPFM) to study switching behaviors.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00056-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5013199","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":"Fractal dimension analysis as an easy computational approach to improve breast cancer histopathological diagnosis","authors":"Lucas Glaucio da Silva,&nbsp;Waleska Rayanne Sizinia da Silva Monteiro,&nbsp;Tiago Medeiros de Aguiar Moreira,&nbsp;Maria Aparecida Esteves Rabelo,&nbsp;Emílio Augusto Campos Pereira de Assis,&nbsp;Gustavo Torres de Souza","doi":"10.1186/s42649-021-00055-w","DOIUrl":"https://doi.org/10.1186/s42649-021-00055-w","url":null,"abstract":"<p>Histopathology is a well-established standard diagnosis employed for the majority of malignancies, including breast cancer. Nevertheless, despite training and standardization, it is considered operator-dependent and errors are still a concern. Fractal dimension analysis is a computational image processing technique that allows assessing the degree of complexity in patterns. We aimed here at providing a robust and easily attainable method for introducing computer-assisted techniques to histopathology laboratories. Slides from two databases were used: A) Breast Cancer Histopathological; and B) Grand Challenge on Breast Cancer Histology. Set A contained 2480 images from 24 patients with benign alterations, and 5429 images from 58 patients with breast cancer. Set B comprised 100 images of each type: normal tissue, benign alterations, in situ carcinoma, and invasive carcinoma. All images were analyzed with the FracLac algorithm in the ImageJ computational environment to yield the box count fractal dimension (Db) results. Images on set A on 40x magnification were statistically different (<i>p</i>?=?0.0003), whereas images on 400x did not present differences in their means. On set B, the mean Db values presented promissing statistical differences when comparing. Normal and/or benign images to in situ and/or invasive carcinoma (all <i>p</i>?&lt;?0.0001). Interestingly, there was no difference when comparing normal tissue to benign alterations. These data corroborate with previous work in which fractal analysis allowed differentiating malignancies. Computer-aided diagnosis algorithms may beneficiate from using Db data; specific Db cut-off values may yield ~?99% specificity in diagnosing breast cancer. Furthermore, the fact that it allows assessing tissue complexity, this tool may be used to understand the progression of the histological alterations in cancer.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00055-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5138975","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":"Morphology and histology of the olfactory organ of two African lungfishes, Protopterus amphibius and P. dolloi (Lepidosirenidae, Dipnoi)","authors":"Hyun Tae Kim,&nbsp;Jong Young Park","doi":"10.1186/s42649-021-00054-x","DOIUrl":"https://doi.org/10.1186/s42649-021-00054-x","url":null,"abstract":"<p>The olfactory organs of two African lungfishes, <i>Protopterus amphibius</i> and <i>P. dolloi</i>, were investigated using a stereo microscope and a compound light microscope and were described anatomically, histologically, and histochemically. Like other lungfishes, these species present the following general features: i) elongated olfactory chamber (OC), ii) anterior nostril at the ventral tip of the upper lip, iii) posterior nostril on the palate of the oral cavity, iv) lamellae with multiple cell types such as olfactory receptor neurons, supporting cells, basal cells, lymphatic cells, and mucous cells (MC), and vi) vomero-like epithelial crypt (VEC) made of glandular epithelium (GE) and crypt sensory epithelium. Some of these features exhibit differences between species: MCs are abundant in both the lamellar and inner walls of the OC in <i>P. amphibius</i> but occur only in lamellae in <i>P. dolloi</i>. On the other hand, some between feature differences are consistent across species: the GE of both <i>P. amphibius</i> and <i>P. dolloi</i> is strongly positive for Alcian blue (pH?2.5)-periodic acid Schiff (deep violet coloration), and positive with hematoxylin and eosin and with Masson’s trichrome (reddish-brown staining), unlike the MCs of the two species which stain dark red with both Alcian blue (pH?2.5)-periodic acid Schiff and Masson’s trichrome but respond faintly to hematoxylin and eosin. The differing abundance of MCs in the two lungfishes might reflect different degrees in aerial exposure of the olfactory organ, while the neutral and acid mucopolysaccharide-containing VEC, as indicated by staining properties of the MCs, is evolutionary evidence that <i>P. amphibius</i> and <i>P. dolloi</i> are the closest living relatives to tetrapods, at least in the order Dipnoi.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00054-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4669104","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":"Automated 3D scoring of fluorescence in situ hybridization (FISH) using a confocal whole slide imaging scanner","authors":"Ziv Frankenstein,&nbsp;Naohiro Uraoka,&nbsp;Umut Aypar,&nbsp;Ruth Aryeequaye,&nbsp;Mamta Rao,&nbsp;Meera Hameed,&nbsp;Yanming Zhang,&nbsp;Yukako Yagi","doi":"10.1186/s42649-021-00053-y","DOIUrl":"https://doi.org/10.1186/s42649-021-00053-y","url":null,"abstract":"<p>Fluorescence in situ hybridization (FISH) is a technique to visualize specific DNA/RNA sequences within the cell nuclei and provide the presence, location and structural integrity of genes on chromosomes. A confocal Whole Slide Imaging (WSI) scanner technology has superior depth resolution compared to wide-field fluorescence imaging. Confocal WSI has the ability to perform serial optical sections with specimen imaging, which is critical for 3D tissue reconstruction for volumetric spatial analysis. The standard clinical manual scoring for FISH is labor-intensive, time-consuming and subjective. Application of multi-gene FISH analysis alongside 3D imaging, significantly increase the level of complexity required for an accurate 3D analysis. Therefore, the purpose of this study is to establish automated 3D FISH scoring for z-stack images from confocal WSI scanner. The algorithm and the application we developed, SHIMARIS PAFQ, successfully employs 3D calculations for clear individual cell nuclei segmentation, gene signals detection and distribution of break-apart probes signal patterns, including standard break-apart, and variant patterns due to truncation, and deletion, etc. The analysis was accurate and precise when compared with ground truth clinical manual counting and scoring reported in ten lymphoma and solid tumors cases. The algorithm and the application we developed, SHIMARIS PAFQ, is objective and more efficient than the conventional procedure. It enables the automated counting of more nuclei, precisely detecting additional abnormal signal variations in nuclei patterns and analyzes gigabyte multi-layer stacking imaging data of tissue samples from patients. Currently, we are developing a deep learning algorithm for automated tumor area detection to be integrated with SHIMARIS PAFQ.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00053-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4368631","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":"Ultrastructure of the fertilized egg envelope from Melanotaenia praecox, Melanotaeniidae, Teleostei","authors":"Joon Hyung Sohn,&nbsp;Dong Heui Kim","doi":"10.1186/s42649-021-00052-z","DOIUrl":"https://doi.org/10.1186/s42649-021-00052-z","url":null,"abstract":"<p>We examined the morphology of fertilized egg and ultrastructures of fertilized egg envelopes of dwarf rainbowfish (<i>Melanotaenia praecox</i>) belong to Melanotaeniidae using light and electron microscopes. The fertilized eggs were spherical with adhesive filament, transparent, demersal, and had a narrow perivitelline space and small oil droplets. The size of fertilized egg was 1.02?±?0.18?mm (<i>n</i>?=?30), and there were two kinds of adhesive filament on the fertilized eggs. The long and thick (diameter 12.22?±?0.52?μm, <i>n</i>?=?20) adhesive filaments were only at the area of animal pole, and short and thin (diameter 1.99?±?0.23?μm, <i>n</i>?=?20) adhesive filaments were around the long filaments. A micropyle was conical shaped with adhesive filament and located near the animal pole of egg. The outer surface of fertilized egg was rough side. Also, the total thickness of the fertilized egg envelope was about 7.46?±?0.41?μm (<i>n</i>?=?20), the fertilized egg envelope consisted of two layers, an inner lamellae layer and an outer layer with high electron-density. And the inner layer was 8 layers. Collectively, these morphological characteristics and adhesive property of fertilized egg with adhesive filaments, and ultrastructures of micropyle, outer surface, and section of fertilized egg envelope are showed species specificity.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00052-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4001513","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":"Methods of measuring presynaptic function with fluorescence probes","authors":"Yeseul Jang,&nbsp;Sung Rae Kim,&nbsp;Sung Hoon Lee","doi":"10.1186/s42649-021-00051-0","DOIUrl":"https://doi.org/10.1186/s42649-021-00051-0","url":null,"abstract":"<p>Synaptic vesicles, which are endogenous to neurotransmitters, are involved in exocytosis by active potentials and release neurotransmitters. Synaptic vesicles used in neurotransmitter release are reused via endocytosis to maintain a pool of synaptic vesicles. Synaptic vesicles show different types of exo- and endocytosis depending on animal species, type of nerve cell, and electrical activity. To accurately understand the dynamics of synaptic vesicles, direct observation of synaptic vesicles is required; however, it was difficult to observe synaptic vesicles of size 40–50?nm in living neurons. The exo-and endocytosis of synaptic vesicles was confirmed by labeling the vesicles with a fluorescent agent and measuring the changes in fluorescence intensity. To date, various methods of labeling synaptic vesicles have been proposed, and each method has its own characteristics, strength, and drawbacks. In this study, we introduce methods that can measure presynaptic activity and describe the characteristics of each technique.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00051-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4692533","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":"Atomically sculptured heart in oxide film using convergent electron beam","authors":"Gwangyeob Lee,&nbsp;Seung-Hyub Baek,&nbsp;Hye Jung Chang","doi":"10.1186/s42649-020-00050-7","DOIUrl":"https://doi.org/10.1186/s42649-020-00050-7","url":null,"abstract":"<p>We demonstrate a fabrication of an atomically controlled single-crystal heart-shaped nanostructure using a convergent electron beam in a scanning transmission electron microscope. The delicately controlled e-beam enable epitaxial crystallization of perovskite oxide LaAlO₃ grown out of the relative conductive interface (i.e. 2 dimensional electron gas) between amorphous LaAlO₃/crystalline SrTiO₃.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-020-00050-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4457215","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":"Protective effects of Erythronium japonicum and Corylopsis coreana Uyeki extracts against 1,3-dichloro-2-propanol-induced hepatotoxicity in rats","authors":"Seunghyun Kim,&nbsp;Hee-Ock Boo,&nbsp;Taeho Ahn,&nbsp;Chun-Sik Bae","doi":"10.1186/s42649-020-00049-0","DOIUrl":"https://doi.org/10.1186/s42649-020-00049-0","url":null,"abstract":"<p><i>Erythronium japonicum</i> (<i>E. japonicum</i>) and <i>Corylopsis coreana</i> Uyeki (<i>C. coreana</i> Uyeki, Korean winter hazel) have been shown to significantly decrease 1,3-dichloro-2-propanol (1,3-DCP)-induced generation of reactive oxygen species and CYP2E1 activity in HuH7, human hepatocytes. In this study, we expanded upon the previous study and investigated the effects of <i>E. japonicum and C. coreana</i> Uyeki extracts on 1,3-DCP-induced liver damage in rats. The pre-treatment of rats with these extracts alleviated a decrease in body weight and reduced 1,3-DCP-induced increase in catalytic activities of hepatic enzymes, such as aspartate aminotransferase and alanine aminotransferase, in the serum. Moreover, treatment with the extracts restored the 1,3-DCP-induced decreases in anti-oxidant enzyme activities, such as the activities of superoxide dismutase and catalase, in the rat liver. Histopathological studies also strongly supported the results of enzyme activities. These results suggest a possibility that the extracts of <i>E. japonicum and C. coreana</i> Uyeki can be a remedy for alleviating 1,3-DCP-induced liver damage in animals.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"50 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-020-00049-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4075462","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":"Mechanical removal of surface residues on graphene for TEM characterizations","authors":"Dong-Gyu Kim,&nbsp;Sol Lee,&nbsp;Kwanpyo Kim","doi":"10.1186/s42649-020-00048-1","DOIUrl":"https://doi.org/10.1186/s42649-020-00048-1","url":null,"abstract":"<p>Contamination on two-dimensional (2D) crystal surfaces poses serious limitations on fundamental studies and applications of 2D crystals. Surface residues induce uncontrolled doping and charge carrier scattering in 2D crystals, and trapped residues in mechanically assembled 2D vertical heterostructures often hinder coupling between stacked layers. Developing a process that can reduce the surface residues on 2D crystals is important. In this study, we explored the use of atomic force microscopy (AFM) to remove surface residues from 2D crystals. Using various transmission electron microscopy (TEM) investigations, we confirmed that surface residues on graphene samples can be effectively removed via contact-mode AFM scanning. The mechanical cleaning process dramatically increases the residue-free areas, where high-resolution imaging of graphene layers can be obtained. We believe that our mechanical cleaning process can be utilized to prepare high-quality 2D crystal samples with minimum surface residues.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"50 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7818295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5168204","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":"Sequential conversion from line defects to atomic clusters in monolayer WS2","authors":"Gyeong Hee Ryu,&nbsp;Ren-Jie Chan","doi":"10.1186/s42649-020-00047-2","DOIUrl":"https://doi.org/10.1186/s42649-020-00047-2","url":null,"abstract":"<p>Transition metal dichalcogenides (TMD), which is composed of a transition metal atom and chalcogen ion atoms, usually form vacancies based on the knock-on threshold of each atom. In particular, when electron beam is irradiated on a monolayer TMD such as MoS₂ and WS₂, S vacancies are formed preferentially, and they are aligned linearly to constitute line defects. And then, a hole is formed at the point where the successively formed line defects collide, and metal clusters are also formed at the edge of the hole. This study reports a process in which the line defects formed in a monolayer WS₂ sheet expends into holes. Here, the process in which the W cluster, which always occurs at the edge of the formed hole, goes through a uniform intermediate phase is explained based on the line defects and the formation behavior of the hole. Further investigation confirms the atomic structure of the intermediate phase using annular dark field scanning transition electron microscopy (ADF-STEM) and image simulation.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"50 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-020-00047-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5168205","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}