scholarly journals Ab initiostructure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

2016 ◽  
Vol 72 (2) ◽  
pp. 236-242 ◽  
Author(s):  
E. van Genderen ◽  
M. T. B. Clabbers ◽  
P. P. Das ◽  
A. Stewart ◽  
I. Nederlof ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Room Temperature ◽  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Direct Methods ◽  
Liquid Nitrogen Temperature ◽  
High Dynamic Range ◽  
Electron Diffraction Data ◽  
High Signal

Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enablingab initiophasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e− Å−2 s−1) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS,SHELX) and for electron crystallography (ADT3D/PETS,SIR2014).

scholarly journals Methods for Voltage-Sensitive Dye Imaging of Rat Cortical Activity With High Signal-to-Noise Ratio

2007 ◽  
Vol 98 (1) ◽  
pp. 502-512 ◽  
Author(s):  
Michael T. Lippert ◽  
Kentaroh Takagaki ◽  
Weifeng Xu ◽  
Xiaoying Huang ◽  
Jian-Young Wu
Keyword(s):  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Field Potential ◽  
High Sensitivity ◽  
High Dynamic Range ◽  
High Signal ◽  
Blue Dye ◽  
Voltage Sensitive Dye ◽  
Imaging Device

We describe methods to achieve high sensitivity in voltage-sensitive dye (VSD) imaging from rat barrel and visual cortices in vivo with the use of a blue dye RH1691 and a high dynamic range imaging device (photodiode array). With an improved staining protocol and an off-line procedure to remove pulsation artifact, the sensitivity of VSD recording is comparable with that of local field potential recording from the same location. With this sensitivity, one can record from ∼500 individual detectors, each covering an area of cortical tissue 160 μm in diameter (total imaging field ∼4 mm in diameter) and a temporal resolution of 1,600 frames/s, without multiple-trial averaging. We can record 80–100 trials of intermittent 10-s trials from each imaging field before the VSD signal reduces to one half of its initial amplitude because of bleaching and wash-out. Taken together, the methods described in this report provide a useful tool for visualizing evoked and spontaneous waves from rodent cortex.

scholarly journals UsingFOCUSto solve zeolite structures from three-dimensional electron diffraction data

2013 ◽  
Vol 46 (4) ◽  
pp. 1017-1023 ◽  
Author(s):  
Stef Smeets ◽  
Lynne B. McCusker ◽  
Christian Baerlocher ◽  
Enrico Mugnaioli ◽  
Ute Kolb
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Direct Methods ◽  
Electron Diffraction Data ◽  
Chemical Information ◽  
Data Sets ◽  
Dimensional Electron ◽  
Specific Chemical ◽  
Structure Solution

The programFOCUS[Grosse-Kunstleve, McCusker & Baerlocher (1997).J. Appl. Cryst.30, 985–995] was originally developed to solve zeolite structures from X-ray powder diffraction data. It uses zeolite-specific chemical information (three-dimensional 4-connected framework structure with known bond distances and angles) to supplement the diffraction data. In this way, it is possible to compensate, at least in part, for the ambiguity of the reflection intensities resulting from reflection overlap, and the program has proven to be quite successful. Recently, advances in electron microscopy have led to the development of automated diffraction tomography (ADT) and rotation electron diffraction (RED) techniques for collecting three-dimensional electron diffraction data on very small crystallites. Reasoning that such data are also less than ideal (dynamical scattering, low completeness, beam damage) and that this can lead to failure of structure solution by conventional direct methods for very complex zeolite frameworks,FOCUSwas modified to accommodate electron diffraction data. The modified program was applied successfully to five different data sets (four ADT and one RED) collected on zeolites of different complexities. One of these could not be solved completely by direct methods but emerged easily in theFOCUStrials.

Generation, Processing, and Transferring of CCD Camera Images in Electron Crystallography

1996 ◽  
Vol 54 ◽  
pp. 426-427
Author(s):  
Z. G. Li ◽  
L. Liang ◽  
R. L. Harlow ◽  
K.E. Lehman ◽  
N. Herron
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Dynamic Range ◽  
Structural Information ◽  
Ccd Camera ◽  
High Dynamic Range ◽  
Electron Diffraction Data ◽  
Electron Crystallography ◽  
Camera Model ◽  
University Of New Mexico

Recently, CCD camera has been more and more used in the electron microscopy particularly for electron crystallography [1]. Use of CCD camera in this field as a recording medium possesses many significant advantages over conventional photographic films. A CCD camera has a very high dynamic range (reliable) and produces images directly in digital form which can be conveniently processed and transferred. We have initiated a program to obtain crystal structural information of plate-like materials by processing electron diffraction data from a CCD detector. As part of our program, we have developed a complete and routine procedure to convert images to diffraction data (h, k, l’s and intensities).Figure 1 is a schematic representation of the procedure. Images are initially obtained using a 1024×1024 Gatan CCD camera (model 794) which was attached to JEM-2000EX electron microscope. The collection of the images is controlled by a MAC computer which also stores the data and allows the data to be viewed. Then, the digitized electron diffraction patterns are transferred to a Sun station computer where, using Khoros software, the CCD images are processed. The Khoros system is a very complete image analysis and image processing software developed by University of New Mexico [2].

scholarly journals REAL-TIME SLAM FOR THE OFF-ROAD AUTONOMOUS DRIVING

2020 ◽  
Vol XLIII-B2-2020 ◽  
pp. 631-635
Author(s):  
B. Vishnyakov ◽  
V. Sheverdin
Keyword(s):  
Dynamic Range ◽  
High Reliability ◽  
Three Dimensional ◽  
Direct Methods ◽  
Autonomous Driving ◽  
High Dynamic Range ◽  
Optimization Method ◽  
Bundle Adjustment ◽  
Measurement Unit ◽  
Natural Environments

Abstract. In this paper we propose a new SLAM algorithm that is robust to the changing environment of the countryside. The hardware part consists of two separate machine vision cameras, joined in stereo, and can be supplemented with LiDAR, IMU and GPS. We introduce a method that can be used to reliably calculate the position of a vehicle in natural environments. To estimate the pose and produce a three-dimensional reconstruction we use a stereo camera rig, inertial measurement unit and the global positioning system. While solving the problem of visual odometry in outdoor scenes we faced a number of difficulties, arising from high dynamic range, as well as the presence of a large number of "similar elements", such as leaves, grass, trees and etc. Under these conditions, it becomes difficult to match feature points in image sequences. HOG-based methods, such as SIFT, SURF and others often do not obtain good matching due to noise, lack of a sufficient number of gradients, and the presence of identical domains. Using neighborhood-based detectors such as DAISY often allows to identify the correct matches, but using them is worth it too expensive. These methods are very demanding on the computational resources and prone to drift. We needed a method that is less expensive, but at the same time provides sufficient accuracy in the trajectory estimation. Direct methods, such as optical flow calculating or direct image matching allow us to map point-to-point in these conditions with high reliability. They also have disadvantages that can be eliminated by using an IMU and modern algorithms. To improve the quality of the algorithms, we solve the reconstruction problem for several frames using the Levenberg-Marquardt optimization method for bundle adjustment. Each pass optimizes frames that are directly related to the last one, we use two threads that perform partial and full optimization of the entire trajectory using graphs to significantly increase the performance of the method.

Automated diffraction tomography combined with electron precession: a new tool for ab initio nanostructure analysis

2009 ◽  
Vol 1184 ◽  
Author(s):  
Ute Kolb ◽  
Tatiana Gorelik ◽  
Enrico Mugnaioli
Keyword(s):  
Electron Diffraction ◽  
Ab Initio ◽  
Crystal Structures ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Direct Methods ◽  
Electron Diffraction Data ◽  
Diffraction Tomography ◽  
Diffraction Mode ◽  
Structure Solution

AbstractThree-dimensional electron diffraction data was collected with our recently developed module for automated diffraction tomography and used to solve inorganic as well as organic crystal structures ab initio. The diffraction data, which covers nearly the full relevant reciprocal space, was collected in the standard nano electron diffraction mode as well as in combination with the precession technique and was subsequently processed with a newly developed automated diffraction analysis and processing software package. Non-precessed data turned out to be sufficient for ab initio structure solution by direct methods for simple crystal structures only, while precessed data allowed structure solution and refinement in all of the studied cases.

scholarly journals Synchrotron X-ray diffraction experiments with a prototype hybrid pixel detector

2011 ◽  
Vol 45 (1) ◽  
pp. 38-47 ◽  
Author(s):  
C. Le Bourlot ◽  
P. Landois ◽  
S. Djaziri ◽  
P.-O. Renault ◽  
E. Le Bourhis ◽  
...  
Keyword(s):  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
High Dynamic Range ◽  
High Signal ◽  
Pixel Detector ◽  
X Ray Diffraction ◽  
X Ray ◽  
Area Detector ◽  
Duplex Steel ◽  
Scientific Results

A prototype X-ray pixel area detector (XPAD3.1) has been used for X-ray diffraction experiments with synchrotron radiation. The characteristics of this detector are very attractive in terms of fast readout time, high dynamic range and high signal-to-noise ratio. The prototype XPAD3.1 enabled various diffraction experiments to be performed at different energies, sample-to-detector distances and detector angles with respect to the direct beam, yet it was necessary to perform corrections on the diffraction images according to the type of experiment. This paper is focused on calibration and correction procedures to obtain high-quality scientific results specifically developed in the context of three different experiments, namely mechanical characterization of nanostructured multilayers, elastic–plastic deformation of duplex steel and growth of carbon nanotubes.

Foundations of Advanced Neuroanatomy: Technical Guidelines for Specimen Preparation, Dissection, and 3D-Photodocumentation in a Surgical Anatomy Laboratory

2019 ◽  
Author(s):  
Luciano César PC Leonel ◽  
Lucas P. Carlstrom ◽  
Christopher S. Graffeo ◽  
Avital Perry ◽  
Carlos Diogenes Pinheiro-Neto ◽  
...  
Keyword(s):  
Oral Tradition ◽  
Dynamic Range ◽  
Tap Water ◽  
Three Dimensional ◽  
High Dynamic Range ◽  
Surgical Anatomy ◽  
Lessons Learned ◽  
Specimen Preparation ◽  
Technological Advances ◽  
Key Steps

Abstract Objective This study was aimed to provide a key update to the seminal works of Prof. Albert L. Rhoton Jr., MD, with particular attention to previously unpublished insights from the oral tradition of his fellows, recent technological advances including endoscopy, and high-dynamic range (HDR) photodocumentation, and, local improvements in technique, we have developed to optimize efficient neuroanatomic study. Methods Two formaldehyde-fixed cadaveric heads were injected with colored latex to demonstrate step-by-step specimen preparation for microscopic or endoscopic dissection. One formaldehyde-fixed brain was utilized to demonstrate optimal three-dimensional (3D) photodocumentation techniques. Results Key steps of specimen preparation include vessel cannulation and securing, serial tap water flushing, specimen drainage, vessel injection with optimized and color-augmented latex material, and storage in 70% ethanol. Optimizations for photodocumentation included the incorporation of dry black drop cloth and covering materials, an imaging-oriented approach to specimen positioning and illumination, and single-camera stereoscopic capture techniques, emphasizing the three-exposure-times-per-eye approach to generating images for HDR postprocessing. Recommended tools, materials, and technical nuances were emphasized throughout. Relative advantages and limitations of major 3D projection systems were comparatively assessed, with sensitivity to audience size and purpose specific recommendations. Conclusion We describe the first consolidated step-by-step approach to advanced neuroanatomy, including specimen preparation, dissection, and 3D photodocumentation, supplemented by previously unpublished insights from the Rhoton fellowship experience and lessons learned in our laboratories in the past years such that Prof. Rhoton's model can be realized, reproduced, and expanded upon in surgical neuroanatomy laboratories worldwide.

scholarly journals Quantitative High-Dynamic-Range Electron Diffraction of Polar Nanodomains in Pb2 ScTaO6

2018 ◽  
Vol 31 (5) ◽  
pp. 1806498 ◽  
Author(s):  
Jonathan J. P. Peters ◽  
Ana M. Sanchez ◽  
David Walker ◽  
Roger Whatmore ◽  
Richard Beanland
Keyword(s):  
Electron Diffraction ◽  
Dynamic Range ◽  
High Dynamic Range ◽  
High Dynamic

scholarly journals Serial Electron Diffraction Data Processing With diffractem and CrystFEL

2021 ◽  
Vol 8 ◽  
Author(s):  
Robert Bücker ◽  
Pascal Hogan-Lamarre ◽  
R. J. Dwayne Miller
Keyword(s):  
Electron Diffraction ◽  
Data Processing ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
New Techniques ◽  
X Ray ◽  
X Ray Crystallography ◽  
Level Of Automation ◽  
Rotation Method ◽  
High Level

Serial electron diffraction (SerialED) is an emerging technique, which applies the snapshot data-collection mode of serial X-ray crystallography to three-dimensional electron diffraction (3D Electron Diffraction), forgoing the conventional rotation method. Similarly to serial X-ray crystallography, this approach leads to almost complete absence of radiation damage effects even for the most sensitive samples, and allows for a high level of automation. However, SerialED also necessitates new techniques of data processing, which combine existing pipelines for rotation electron diffraction and serial X-ray crystallography with some more particular solutions for challenges arising in SerialED specifically. Here, we introduce our analysis pipeline for SerialED data, and its implementation using the CrystFEL and diffractem program packages. Detailed examples are provided in extensive supplementary code.

Sign in / Sign up

Export Citation Format

Share Document