Removing constraints of 4D-STEM with a framework for event-driven acquisition and processing.

Preparation of damage-free kerogen specimen for microscopy: Understanding the damage mechanisms induced by ion milling techniques

One of the primary uses for transmission electron microscopy (TEM) is to measure diffraction pattern images in order to determine a crystal structure and orientation. In nanobeam electron diffraction (NBED), we scan a moderately converged electron probe over the sample to acquire thousands or even millions of sequential diffraction images, a technique that is especially appropriate for polycrystalline samples. However, due to the large Ewald sphere of TEM, excitation of Bragg peaks can be extremely sensitive to sample tilt, varying strongly for even a few degrees of sample tilt for crystalline samples. In this paper, we present multibeam electron diffraction (MBED), where multiple probe-forming apertures are used to create multiple scanning transmission electron microscopy (STEM) probes, all of which interact with the sample simultaneously. We detail designs for MBED experiments, and a method for using a focused ion beam to produce MBED apertures. We show the efficacy of the MBED technique for crystalline orientation mapping using both simulations and proof-of-principle experiments. We also show how the angular information in MBED can be used to perform 3D tomographic reconstruction of samples without needing to tilt or scan the sample multiple times. Finally, we also discuss future opportunities for the MBED method.

Domain patterns consisting of triangular nanodomains of less than 50 nm size, arranged into long regular vertex arrays separated by stripe domains, were observed by (scanning and high-resolution) transmission electron microscopy and piezoresponse force microscopy in BiFeO${}_{3}$ single crystals grown from solution flux. Piezoresponse force microscopy analysis together with crystallographic analysis by selected area and nanobeam electron diffraction indicate that these patterns consist of ferroelectric 109${}^{\ensuremath{\circ}}$ domains. A possibility for conserving Kittel's law is discussed in terms of the patterns being confined to the skin layer observed recently on BiFeO${}_{3}$ single crystals.

Even though minicomputers and microcomputers are larger and faster than ever before, they have not kept pace with the demands of telemetry users. Hardware preprocessor of telemetry data has been used in distributed telemetry computer system for processing all data at extremely high rates. According to the requirements and characteristics of telemetry data processing, a distributed multiple data stream hardware preprocessor with multiplex microcomputers of telemetry data is introduced in the paper. Each data stream is processed by three microcomputer models coupled in multi-computation architecture. The microcomputer models consist of TMS320C25 in the preprocessor. The preprocessor owns the features of wavefront array processors. A time-wait procedure can be done in pipeline processing and large data processing can be derived in parallel processing and pipeline processing. >

Effect of training sample size, image resolution and epochs on filamentous and floc-forming bacteria classification using machine learning.

Extracting moving shapes by evidence gathering

Computing aspects of molecular dynamics simulation

Abnormal accumulation of brain metals is a key feature of Alzheimer’s disease (AD). Formation of amyloid-β plaque cores (APC) is related to interactions with biometals, especially Fe, Cu and Zn, but their particular structural associations and roles remain unclear. Using an integrative set of advanced transmission electron microscopy (TEM) techniques, including spherical aberration-corrected scanning transmission electron microscopy (Cs-STEM), nano-beam electron diffraction, electron holography and analytical spectroscopy techniques (EDX and EELS), we demonstrate that Fe in APC is present as iron oxide (Fe3O4) magnetite nanoparticles. Here we show that Fe was accumulated primarily as nanostructured particles within APC, whereas Cu and Zn were distributed through the amyloid fibers. Remarkably, these highly organized crystalline magnetite nanostructures directly bound into fibrillar Aβ showed characteristic superparamagnetic responses with saturated magnetization with circular contours, as observed for the first time by off-axis electron holography of nanometer scale particles.

In this study, we introduced the method for the growth of titanium molybdenum oxide (TMO) nanotubes directly from metallic precursor solid state solution and provided their structural and chemical characterization. Precursor films with content of molybdenum from 32 to 82 at% were prepared using co-deposition magnetron sputtering. The optimization of deposition parameters allowed for the growth of a continuous nanotube array with a length up to 700 nm ± 10% by anodic oxidation. Scanning electron microscopy (SEM) combined with energy-dispersive spectroscopy (EDS) revealed nanotube formation with Ti1−xMoxO2 composition, where x can reach the value of 0.5. Scanning transmission electron microscopy combined with EDS (STEM-EDS) confirmed the incorporation of Mo into the TiO2 lattice and uniform elemental distribution across the nanotube at the submicron level. The nanobeam electron diffraction (NBD) and X-ray diffraction analyses (XRD) did not show any notable crystal phase formation for the titanium molybdenum oxide phase.

Last year, the X27A beamline at the National Synchrotron Light Source (NSLS) became dedicated solely to X-Ray Computed Microtomography (XCMT). This is a third-generation instrument capable of producing tomographic volumes of 1 - 2 micron resolution over a 2 - 3 mm field of view. Recent enhancements will be discussed. These have focused on two issues: the desire for real-time data acquisition and processing and the need for highly monochromatic beam (.1% energy bandpass). The latter will permit k-edge subtraction studies and will provide improved image contrast from below the Cr (6 keV) up to the Cs (36 keV) k-edge. A range of applications that benefit from these improvements will be discussed as well. These two goals are somewhat counterproductive, however; higher monochromaticity yields a lower flux forcing longer data acquisition times. To balance the two, a more efficient scintillator for X-ray conversion is being developed. Some testing of a prototype scintillator has been performed; preliminary results will be presented here. In the meantime, data reconstruction times have been reduced, and the entire tomographic acquisition, reconstruction and volume rendering process streamlined to make efficient use of synchrotron beam time. A Fast Filtered Back Transform (FFBT) reconstruction program recently developed helped to reduce the time to reconstruct a volume of 150 X 150 X 250 pixels3 (over 5 million voxels) from the raw camera data to 1.5 minutes on a dual R10,000 CPU. With these improvements, one can now obtain a 'quick look' of a small tomographic volume (approximately 106 voxels) in just over 15 minutes from the start of data acquisition.© (1999) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

RNA-sequencing (RNA-seq) has become an established way for measuring gene expression in model organisms and humans. While methods development for refining the corresponding data processing and analysis pipeline is ongoing, protocols for typical steps have been proposed and are widely used. Several user interfaces have been developed for making such analysis steps accessible to life scientists without extensive knowledge of command line tools. We performed a systematic search and evaluation of such interfaces to investigate to what extent these can indeed facilitate RNA-seq data analysis. We found a total of 29 open source interfaces, and six of the more widely used interfaces were evaluated in detail. Central criteria for evaluation were ease of configuration, documentation, usability, computational demand and reporting. No interface scored best in all of these criteria, indicating that the final choice will depend on the specific perspective of users and the corresponding weighting of criteria. Considerable technical hurdles had to be overcome in our evaluation. For many users, this will diminish potential benefits compared with command line tools, leaving room for future improvement of interfaces.

WITHDRAWN: SIMPLE 3.0. Stream single-particle cryo-EM analysis in real time

In scanning transmission electron microscopy (STEM), one can obtain a variety of STEM images such as bright‐field (BF) and annular dark‐field (ADF) STEM images by changing the shape of the scintillator. However, the intensity distribution of convergent beam electron diffraction (CBED) patterns at the detector plane is yet to be fully utilized. Meanwhile, direct electron detectors with fast frame rate have recently been commercialized and used in electron microscopy. Such detectors, when used for recording CBED pattern images for each STEM probe position, are called pixelated STEM detectors. With the obtained 4‐dimensional (4D) dataset, any shape of STEM detector can be synthesized in a post processing by a free selection of the integration area. Therefore, we can synthesize variety of STEM images such as differential phase contrast (DPC) and annular bright field (ABF) images, if we once record the image signal with a pixelated detector. The 4D dataset can also be used for the advanced image processing techniques such as ptychography, which has been shown to provide high efficiency for reconstructing the phase image of an object [1,2]. Using ptychography, not only the phase contrast can be enhanced but also the effect of lens aberrations to the image such as defocus can be corrected by the post processing using the information collected by a pixelated detector. Experiments were performed using an aberration corrected microscope (JEOL JEM‐ARM200F) equipped with a pixelated detector (pnDetector pnCCD), the fast direct electron detector, which can record images at a speed of 1,000 fps in a full frame mode (264 x 264 pixels). Binning or windowing can increase the speed. The camera was placed below the ADF detector to enable simultaneous recording. Figure 1 shows STEM images of a monolayer graphene obtained at 80 kV. Fig. 1a shows an ADF image obtained with the probe current of approximately 0.2 pA and the dwell time for a pixel of 0.5 ms. Because of a combination of low dose and residual uncorrected aberrations, the lattice contrast of graphene is almost buried in the noise originated from 50 Hz commercial frequency. Fig. 1b shows a reconstructed phase image using ptychography. The image contrast is significantly improved compared to the simultaneous ADF image, but the contrast transfer of the image (see the Fourier transform displayed in the inset) is anisotropic, resulting in uncertain positions of carbon atoms. This is because there remains large two‐fold astigmatism and defocus in the image shown in Fig. 1(b), because we could not adjust those by observation of the ADF image due to the weak image signal. Fig. 1c is a phase image in which the aberrations are corrected through post processing using the same 4D dataset by applying correction functions in the spatial frequency domain. The image is no longer anisotropic and the carbon atomic positions can be unambiguously determined. Although the same amount of electron dose is used to form the ADF and the corrected phase images, the result clearly shows the benefit of ptychographic phase reconstruction in improving image signal to noise and being able to correct aberrations through post processing. Figure 2 shows the ptychographic phase maps of the 4D dataset at a certain spatial frequency. With an aberration‐free electron probe, they would be flat phase on the two sidebands, and the phase difference between the bands be π. In Fig. 2a, the map of the original dataset, there is a phase gradient inside each sideband because the aberrations were present in the electron probe. Fig. 2b is the correction function that compensates for the aberration seen in Fig. 2a. Fig. 2c is the corrected phase map and corresponding to the image in Fig. 1c. Here, only defocus and two‐fold astigmatism are corrected but corrections of other higher order aberrations are in principle possible. Figure 3 shows through focus images created in the same way as above. As we know the full information on the electron wave at the condenser aperture plane, we can induce any aberrations such as defocus.

This paper describes a real-time data collection framework and an adaptive machining learning method for constructing a real-time energy prediction model for a machine tool. To effectively establish the energy consumption pattern of a machine tool over time, the energy prediction model is continuously updated with new measurement data to account for time-varying effects of the machine tool, such as tool wear and machine tool deterioration. In this work, a real-time data collection and processing framework is developed to retrieve raw data from a milling machine tool and its sensors and convert them into relevant input features. The extracted input features are then used to construct the energy prediction model using Gaussian Process (GP) regression. To update the GP regression model with real-time streaming data, we investigate the use of sparse representation of the covariance matrix to reduce the computational and storage demands of the GP regression. We compare computational efficiency of sparse GP to that of full GP regression model and show the effectiveness of the sparse GP regression model for tracking the variation in the energy consumption pattern of the target machine.

Often real-time systems can run in different modes depending on the external environment or their internal state. Each operational mode is characterized by a set of tasks with different computational demand, resource requirements, and resource availability. When resource reservation is used to achieve temporal isolation among applications, the reservation parameters may need to change from mode to mode. Hence, an additional guarantee is required to ensure feasibility not only of the applications, but also of the reservations. This paper presents a schedulability analysis to predict the timing behavior of a multi-moded resource reservation, whose parameters may change due to a mode transition. Resource provisioning is analyzed in all the operational modes and also during mode-changes in order to guarantee a minimum amount of resources and derive a feasibility condition for realtime applications and reservations. Theoretical results are also illustrated with examples and test cases.