scholarly journals Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time

2016 ◽  
Vol 49 (3) ◽  
pp. 1042-1047 ◽  
Author(s):  
Benedikt J. Daurer ◽  
Max F. Hantke ◽  
Carl Nettelblad ◽  
Filipe R. N. C. Maia
Keyword(s):  
Real Time ◽  
Three Dimensional ◽  
Software Tool ◽  
Immediate Feedback ◽  
X Ray ◽  
High Data ◽  
Real Time Analysis ◽  
X Ray Imaging ◽  
Linac Coherent Light Source ◽  
Diffraction Patterns

Advances in X-ray detectors and increases in the brightness of X-ray sources combined with more efficient sample delivery techniques have brought about tremendous increases in the speed of data collection in diffraction experiments. Using X-ray free-electron lasers such as the Linac Coherent Light Source (LCLS), more than 100 diffraction patterns can be collected in a second. These high data rates are invaluable for flash X-ray imaging (FXI), where aerosolized samples are exposed to the X-ray beam and the resulting diffraction patterns are used to reconstruct a three-dimensional image of the sample. Such experiments require immediate feedback on the quality of the data collected to adjust or validate experimental parameters, such as aerosol injector settings, beamline geometry or sample composition. The scarcity of available beamtime at the laser facilities makes any delay extremely costly. This paper presentsHummingbird, an open-source scalable Python-based software tool for real-time analysis of diffraction data with the purpose of giving users immediate feedback during their experiments.Hummingbirdprovides a fast, flexible and easy-to-use framework. It has already proven to be of great value in numerous FXI experiments at the LCLS.

scholarly journals Femtosecond X-ray diffraction from two-dimensional protein crystals

IUCrJ ◽  
2014 ◽  
Vol 1 (2) ◽  
pp. 95-100 ◽  
Author(s):  
Matthias Frank ◽  
David B. Carlson ◽  
Mark S. Hunter ◽  
Garth J. Williams ◽  
Marc Messerschmidt ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Bragg Diffraction ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Linac Coherent Light Source ◽  
Diffraction Patterns ◽  
Better Than

X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

scholarly journals Dragonfly: an implementation of the expand–maximize–compress algorithm for single-particle imaging

2016 ◽  
Vol 49 (4) ◽  
pp. 1320-1335 ◽  
Author(s):  
Kartik Ayyer ◽  
Ti-Yen Lan ◽  
Veit Elser ◽  
N. Duane Loh
Keyword(s):  
Single Particle ◽  
Parallel Implementation ◽  
Three Dimensional ◽  
Reconstruction Algorithm ◽  
X Ray ◽  
Resultant Data ◽  
Linac Coherent Light Source ◽  
Diffraction Patterns ◽  
Particle Imaging ◽  
Single Particle Imaging

Single-particle imaging (SPI) with X-ray free-electron lasers has the potential to change fundamentally how biomacromolecules are imaged. The structure would be derived from millions of diffraction patterns, each from a different copy of the macromolecule before it is torn apart by radiation damage. The challenges posed by the resultant data stream are staggering: millions of incomplete, noisy and un-oriented patterns have to be computationally assembled into a three-dimensional intensity map and then phase reconstructed. In this paper, theDragonflysoftware package is described, based on a parallel implementation of the expand–maximize–compress reconstruction algorithm that is well suited for this task. Auxiliary modules to simulate SPI data streams are also included to assess the feasibility of proposed SPI experiments at the Linac Coherent Light Source, Stanford, California, USA.

scholarly journals Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses

IUCrJ ◽  
2017 ◽  
Vol 4 (3) ◽  
pp. 251-262 ◽  
Author(s):  
Benedikt J. Daurer ◽  
Kenta Okamoto ◽  
Johan Bielecki ◽  
Filipe R. N. C. Maia ◽  
Kerstin Mühlig ◽  
...  
Keyword(s):  
Size Distribution ◽  
Small Samples ◽  
Reduced Pressure ◽  
X Ray ◽  
X Ray Imaging ◽  
Linac Coherent Light Source ◽  
Phase Variations ◽  
Diffraction Patterns ◽  
Imaging Instrument ◽  
Individual Particles

This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. AerosolizedOmono River virusparticles of ∼40 nm in diameter were injected into the submicrometre X-ray focus at a reduced pressure. Diffraction patterns were recorded on two area detectors. The statistical nature of the measurements from many individual particles provided information about the intensity profile of the X-ray beam, phase variations in the wavefront and the size distribution of the injected particles. The results point to a wider than expected size distribution (from ∼35 to ∼300 nm in diameter). This is likely to be owing to nonvolatile contaminants from larger droplets during aerosolization and droplet evaporation. The results suggest that the concentration of nonvolatile contaminants and the ratio between the volumes of the initial droplet and the sample particles is critical in such studies. The maximum beam intensity in the focus was found to be 1.9 × 1012photons per µm2per pulse. The full-width of the focus at half-maximum was estimated to be 500 nm (assuming 20% beamline transmission), and this width is larger than expected. Under these conditions, the diffraction signal from a sample-sized particle remained above the average background to a resolution of 4.25 nm. The results suggest that reducing the size of the initial droplets during aerosolization is necessary to bring small particles into the scope of detailed structural studies with X-ray lasers.

An Interactive Minicomputer Program for the Indexing and Simulation of Electron Diffraction Patterns

1976 ◽  
Vol 34 ◽  
pp. 542-543
Author(s):  
R.P. Goehner ◽  
W.T. Hatfield ◽  
Prakash Rao
Keyword(s):  
Electron Diffraction ◽  
Real Time ◽  
Pattern Analysis ◽  
Flow Diagram ◽  
Hard Copy ◽  
Time Analysis ◽  
Real Time Analysis ◽  
Transmission Electron ◽  
One Step ◽  
Diffraction Patterns

Computer programs are now available in various laboratories for the indexing and simulation of transmission electron diffraction patterns. Although these programs address themselves to the solution of various aspects of the indexing and simulation process, the ultimate goal is to perform real time diffraction pattern analysis directly off of the imaging screen of the transmission electron microscope. The program to be described in this paper represents one step prior to real time analysis. It involves the combination of two programs, described in an earlier paper(l), into a single program for use on an interactive basis with a minicomputer. In our case, the minicomputer is an INTERDATA 70 equipped with a Tektronix 4010-1 graphical display terminal and hard copy unit.A simplified flow diagram of the combined program, written in Fortran IV, is shown in Figure 1. It consists of two programs INDEX and TEDP which index and simulate electron diffraction patterns respectively. The user has the option of choosing either the indexing or simulating aspects of the combined program.

A Magnetically Guided Self‐Rolled Microrobot for Targeted Drug Delivery, Real‐Time X‐Ray Imaging, and Microrobot Retrieval

2021 ◽  
pp. 2001681
Author(s):  
Kim Tien Nguyen ◽  
Gwangjun Go ◽  
Zhen Jin ◽  
Bobby Aditya Darmawan ◽  
Ami Yoo ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Real Time ◽  
Targeted Drug Delivery ◽  
X Ray ◽  
X Ray Imaging ◽  
Targeted Drug

2D X-ray diffraction and molecular modelling of the crystalline structure of polyesters under uniaxial stress

2021 ◽  
pp. 096739112199822
Author(s):  
Ahmed I Abou-Kandil ◽  
Gerhard Goldbeck
Keyword(s):  
Crystalline Structure ◽  
Molecular Modelling ◽  
Three Dimensional ◽  
Uniaxial Stress ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range ◽  
Modelling Techniques ◽  
Diffraction Patterns

Studying the crystalline structure of uniaxially and biaxially drawn polyesters is of great importance due to their wide range of applications. In this study, we shed some light on the behaviour of PET and PEN under uniaxial stress using experimental and molecular modelling techniques. Comparing experiment with modelling provides insights into polymer crystallisation with extended chains. Experimental x-ray diffraction patterns are reproduced by means of models of chains sliding along the c-axis leading to some loss of three-dimensional order, i.e. moving away from the condition of perfect register of the fully extended chains in triclinic crystals of both PET and PEN. This will help us understand the mechanism of polymer crystallisation under uniaxial stress and the appearance of mesophases in some cases as discussed herein.

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