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- ItemOptimal principal component analysis of stem xeds spectrum images(Heidelberg : Springer Verlag, 2019) Potapov, P.; Lubk, A.STEM XEDS spectrum images can be drastically denoised by application of the principal component analysis (PCA). This paper looks inside the PCA workflow step by step on an example of a complex semiconductor structure consisting of a number of different phases. Typical problems distorting the principal components decomposition are highlighted and solutions for the successful PCA are described. Particular attention is paid to the optimal truncation of principal components in the course of reconstructing denoised data. A novel accurate and robust method, which overperforms the existing truncation methods is suggested for the first time and described in details.
- ItemStudying dynamic processes of nano-sized objects in liquid using scanning transmission electron microscopy(Cambridge : JoVE, 2017) de Jong, Niels; Hermannsdörfer, JustusSamples fully embedded in liquid can be studied at a nanoscale spatial resolution with Scanning Transmission Electron Microscopy (STEM) using a microfluidic chamber assembled in the specimen holder for Transmission Electron Microscopy (TEM) and STEM. The microfluidic system consists of two silicon microchips supporting thin Silicon Nitride (SiN) membrane windows. This article describes the basic steps of sample loading and data acquisition. Most important of all is to ensure that the liquid compartment is correctly assembled, thus providing a thin liquid layer and a vacuum seal. This protocol also includes a number of tests necessary to perform during sample loading in order to ensure correct assembly. Once the sample is loaded in the electron microscope, the liquid thickness needs to be measured. Incorrect assembly may result in a too-thick liquid, while a too-thin liquid may indicate the absence of liquid, such as when a bubble is formed. Finally, the protocol explains how images are taken and how dynamic processes can be studied. A sample containing AuNPs is imaged both in pure water and in saline.
- ItemStudying the Stoichiometry of Epidermal Growth Factor Receptor in Intact Cells using Correlative Microscopy([S.l.] : [s.n.], 2015) Peckys, Diana B.; de Jonge, NielsThis protocol describes the labeling of epidermal growth factor receptor (EGFR) on COS7 fibroblast cells, and subsequent correlative fluorescence microscopy and environmental scanning electron microscopy (ESEM) of whole cells in hydrated state. Fluorescent quantum dots (QDs) were coupled to EGFR via a two-step labeling protocol, providing an efficient and specific protein labeling, while avoiding label-induced clustering of the receptor. Fluorescence microscopy provided overview images of the cellular locations of the EGFR. The scanning transmission electron microscopy (STEM) detector was used to detect the QD labels with nanoscale resolution. The resulting correlative images provide data of the cellular EGFR distribution, and the stoichiometry at the single molecular level in the natural context of the hydrated intact cell. ESEM-STEM images revealed the receptor to be present as monomer, as homodimer, and in small clusters. Labeling with two different QDs, i.e., one emitting at 655 nm and at 800 revealed similar characteristic results.
- ItemElectron Tomography of Pencil-Shaped GaN/(In,Ga)N Core-Shell Nanowires(New York, NY [u.a.] : Springer, 2019) Nicolai, Lars; Gačević, Žarko; Calleja, Enrique; Trampert, AchimThe three-dimensional structure of GaN/(In,Ga)N core-shell nanowires with multi-faceted pencil-shaped apex is analyzed by electron tomography using high-angle annular dark-field mode in a scanning transmission electron microscope. Selective area growth on GaN-on-sapphire templates using a patterned mask is performed by molecular beam epitaxy to obtain ordered arrays of uniform nanowires. Our results of the tomographic reconstruction allow the detailed determination of the complex morphology of the inner (In,Ga)N multi-faceted shell structure and its deviation from the perfect hexagonal symmetry. The tomogram unambiguously identifies a dot-in-a-wire configuration at the nanowire apex including the exact shape and size, as well as the spatial distribution of its chemical composition. © 2019, The Author(s).
- ItemAntiphase Boundaries Constitute Fast Cation Diffusion Paths in SrTiO3 Memristive Devices(Weinheim : Wiley-VCH, 2020) Heisig, Thomas; Kler, Joe; Du, Hongchu; Baeumer, Christoph; Hensling, Felix; Glöß, Maria; Moors, Marco; Locatelli, Andrea; Menteş, Tevfik Onur; Genuzio, Francesca; Mayer, Joachim; De Souza, Roger A.; Dittmann, ReginaResistive switching in transition metal oxide-based metal-insulator-metal structures relies on the reversible drift of ions under an applied electric field on the nanoscale. In such structures, the formation of conductive filaments is believed to be induced by the electric-field driven migration of oxygen anions, while the cation sublattice is often considered to be inactive. This simple mechanistic picture of the switching process is incomplete as both oxygen anions and metal cations have been previously identified as mobile species under device operation. Here, spectromicroscopic techniques combined with atomistic simulations to elucidate the diffusion and drift processes that take place in the resistive switching model material SrTiO3 are used. It is demonstrated that the conductive filament in epitaxial SrTiO3 devices is not homogenous but exhibits a complex microstructure. Specifically, the filament consists of a conductive Ti3+-rich region and insulating Sr-rich islands. Transmission electron microscopy shows that the Sr-rich islands emerge above Ruddlesden–Popper type antiphase boundaries. The role of these extended defects is clarified by molecular static and molecular dynamic simulations, which reveal that the Ruddlesden–Popper antiphase boundaries constitute diffusion fast-paths for Sr cations in the perovskites structure. © 2020 The Authors. Published by Wiley-VCH GmbH
- ItemVisualisation of HER2 homodimers in single cells from HER2 overexpressing primary formalin fixed paraffin embedded tumour tissue(London : BioMed Central, 2019) Peckys, D.B.; Hirsch, D.; Gaiser, T.; De, Jonge, N.Background: HER2 is considered as one of the most important, predictive biomarkers in oncology. The diagnosis of HER2 positive cancer types such as breast- and gastric cancer is usually based on immunohistochemical HER2 staining of tumour tissue. However, the current immunohistochemical methods do not provide localized information about HER2's functional state. In order to generate signals leading to cell growth and proliferation, the receptor spontaneously forms homodimers, a process that can differ between individual cancer cells. Materials and methods: HER2 overexpressing tumour cells were dissociated from formalin-fixed paraffin-embedded (FFPE) patient's biopsy sections, subjected to a heat-induced antigen retrieval procedure, and immobilized on microchips. HER2 was specifically labelled via a two-step protocol involving the incubation with an Affibody-biotin compound followed by the binding of a streptavidin coated quantum dot (QD) nanoparticle. Cells with membrane bound HER2 were identified using fluorescence microscopy, coated with graphene to preserve their hydrated state, and subsequently examined by scanning transmission electron microscopy (STEM) to obtain the locations at the single molecule level. Label position data was statistically analysed via the pair correlation function, yielding information about the presence of HER2 homodimers. Results: Tumour cells from two biopsies, scored HER2 3+, and a HER2 negative control sample were examined. The specific labelling protocol was first tested for a sectioned tissue sample of HER2-overexpressing tumour. Subsequently, a protocol was optimized to study HER2 homodimerization in single cells dissociated from the tissue section. Electron microscopy data showed membrane bound HER2 in average densities of 201-689 proteins/μm2. An automated, statistical analysis of well over 200,000 of measured protein positions revealed the presence of HER2 homodimers in 33 and 55% of the analysed images for patient 1 and 2, respectively. Conclusions: We introduced an electron microscopy method capable of measuring the positions of individually labelled HER2 proteins in patient tumour cells from which information about the functional status of the receptor was derived. This method could take HER2 testing a step further by examining HER2 homodimerization directly out of tumour tissue and may become important for adjusting a personalized antibody-based drug therapy. © 2019 The Author(s).