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  • International Union of Crystallography (IUCr)  (8)
  • 1
    In: IUCrJ, International Union of Crystallography (IUCr), Vol. 4, No. 3 ( 2017-05-01), p. 251-262
    Abstract: 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. Aerosolized Omono River virus particles 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 × 10 12 photons per µm 2 per 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.
    Type of Medium: Online Resource
    ISSN: 2052-2525
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2017
    detail.hit.zdb_id: 2754953-7
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  • 2
    In: IUCrJ, International Union of Crystallography (IUCr), Vol. 6, No. 3 ( 2019-05-01), p. 500-500
    Abstract: Corrections to the article by Daurer et al. [ IUCrJ (2017). 4 , 251–262] are given.
    Type of Medium: Online Resource
    ISSN: 2052-2525
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2019
    detail.hit.zdb_id: 2754953-7
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  • 3
    In: IUCrJ, International Union of Crystallography (IUCr), Vol. 5, No. 5 ( 2018-09-01), p. 531-541
    Abstract: Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.
    Type of Medium: Online Resource
    ISSN: 2052-2525
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2018
    detail.hit.zdb_id: 2754953-7
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  • 4
    In: IUCrJ, International Union of Crystallography (IUCr), Vol. 5, No. 6 ( 2018-11-01), p. 673-680
    Abstract: Ultra-bright femtosecond X-ray pulses generated by X-ray free-electron lasers (XFELs) can be used to image high-resolution structures without the need for crystallization. For this approach, aerosol injection has been a successful method to deliver 70–2000 nm particles into the XFEL beam efficiently and at low noise. Improving the technique of aerosol sample delivery and extending it to single proteins necessitates quantitative aerosol diagnostics. Here a lab-based technique is introduced for Rayleigh-scattering microscopy allowing us to track and size aerosolized particles down to 40 nm in diameter as they exit the injector. This technique was used to characterize the `Uppsala injector', which is a pioneering and frequently used aerosol sample injector for XFEL single-particle imaging. The particle-beam focus, particle velocities, particle density and injection yield were measured at different operating conditions. It is also shown how high particle densities and good injection yields can be reached for large particles (100–500 nm). It is found that with decreasing particle size, particle densities and injection yields deteriorate, indicating the need for different injection strategies to extend XFEL imaging to smaller targets, such as single proteins. This work demonstrates the power of Rayleigh-scattering microscopy for studying focused aerosol beams quantitatively. It lays the foundation for lab-based injector development and online injection diagnostics for XFEL research. In the future, the technique may also find application in other fields that employ focused aerosol beams, such as mass spectrometry, particle deposition, fuel injection and three-dimensional printing techniques.
    Type of Medium: Online Resource
    ISSN: 2052-2525
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2018
    detail.hit.zdb_id: 2754953-7
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  • 5
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2016
    In:  Journal of Applied Crystallography Vol. 49, No. 3 ( 2016-06-01), p. 1042-1047
    In: Journal of Applied Crystallography, International Union of Crystallography (IUCr), Vol. 49, No. 3 ( 2016-06-01), p. 1042-1047
    Abstract: 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 presents Hummingbird , 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. Hummingbird provides a fast, flexible and easy-to-use framework. It has already proven to be of great value in numerous FXI experiments at the LCLS.
    Type of Medium: Online Resource
    ISSN: 1600-5767
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2016
    detail.hit.zdb_id: 2020879-0
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  • 6
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2020
    In:  Journal of Applied Crystallography Vol. 53, No. 4 ( 2020-08-01), p. 949-956
    In: Journal of Applied Crystallography, International Union of Crystallography (IUCr), Vol. 53, No. 4 ( 2020-08-01), p. 949-956
    Abstract: The pressing need for knowledge of the detailed wavefront properties of ultra-bright and ultra-short pulses produced by free-electron lasers has spurred the development of several complementary characterization approaches. Here a method based on ptychography is presented that can retrieve high-resolution complex-valued wavefunctions of individual pulses without strong constraints on the illumination or sample object used. The technique is demonstrated within experimental conditions suited for diffraction experiments and exploiting Kirkpatrick–Baez focusing optics. This lensless technique, applicable to many other short-pulse instruments, can achieve diffraction-limited resolution.
    Type of Medium: Online Resource
    ISSN: 1600-5767
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2020
    detail.hit.zdb_id: 2020879-0
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  • 7
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2016
    In:  Journal of Applied Crystallography Vol. 49, No. 4 ( 2016-08-01), p. 1356-1362
    In: Journal of Applied Crystallography, International Union of Crystallography (IUCr), Vol. 49, No. 4 ( 2016-08-01), p. 1356-1362
    Abstract: Flash X-ray imaging has the potential to determine structures down to molecular resolution without the need for crystallization. The ability to accurately predict the diffraction signal and to identify the optimal experimental configuration within the limits of the instrument is important for successful data collection. This article introduces Condor , an open-source simulation tool to predict X-ray far-field scattering amplitudes of isolated particles for customized experimental designs and samples, which the user defines by an atomic or a refractive index model. The software enables researchers to test whether their envisaged imaging experiment is feasible, and to optimize critical parameters for reaching the best possible result. It also aims to support researchers who intend to create or advance reconstruction algorithms by simulating realistic test data. Condor is designed to be easy to use and can be either installed as a Python package or used from its web interface (http://lmb.icm.uu.se/condor). X-ray free-electron lasers have high running costs and beam time at these facilities is precious. Data quality can be substantially improved by using simulations to guide the experimental design and simplify data analysis.
    Type of Medium: Online Resource
    ISSN: 1600-5767
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2016
    detail.hit.zdb_id: 2020879-0
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  • 8
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2014
    In:  Journal of Applied Crystallography Vol. 47, No. 3 ( 2014-06-01), p. 1118-1131
    In: Journal of Applied Crystallography, International Union of Crystallography (IUCr), Vol. 47, No. 3 ( 2014-06-01), p. 1118-1131
    Abstract: The emerging technique of serial X-ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X-ray source at repetition rates of 100 Hz or higher, has necessitated the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X-ray free-electron lasers, the software is based on a modular facility-independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.
    Type of Medium: Online Resource
    ISSN: 1600-5767
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2014
    detail.hit.zdb_id: 2020879-0
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