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Condor: a simulation tool for flash X-ray imaging
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
2016 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, 1356-1362 p.Article, review/survey (Refereed) Published
Resource type
Text
Abstract [en]

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.

Place, publisher, year, edition, pages
2016. Vol. 49, 1356-1362 p.
Keyword [en]
femtosecond coherent diffractive imaging, X-ray free-electron lasers, simulation, single-particle imaging, computer programs
National Category
Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-300211DOI: 10.1107/S1600576716009213ISI: 000382755900027OAI: oai:DiVA.org:uu-300211DiVA: diva2:951111
Available from: 2016-08-05 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
In thesis
1. Coherent Diffractive Imaging with X-ray Lasers
Open this publication in new window or tab >>Coherent Diffractive Imaging with X-ray Lasers
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The newly emerging technology of X-ray free-electron lasers (XFELs) has the potential to revolutionise molecular imaging. XFELs generate very intense X-ray pulses and predictions suggest that they may be used for structure determination to atomic resolution even for single molecules. XFELs produce femtosecond pulses that outrun processes of radiation damage and permit the study of structures at room temperature and of structural dynamics.

While the first demonstrations of flash X-ray diffractive imaging (FXI) on biological particles were encouraging, they also revealed technical challenges. In this work we demonstrated how some of these challenges can be overcome. We exemplified, with heterogeneous cell organelles, how tens of thousands of FXI diffraction patterns can be collected, sorted, and analysed in an automatic data processing pipeline. We improved  image resolution and reduced problems with missing data. We validated, described, and deposited the experimental data in the Coherent X-ray Imaging Data Bank.

We demonstrated that aerosol injection can be used to collect FXI data at high hit ratios and with low background. We reduced problems with non-volatile sample contaminants by decreasing aerosol droplet sizes from ~1000 nm to ~150 nm. We achieved this by adapting an electrospray aerosoliser to the Uppsala sample injector. Mie scattering imaging was used as a diagnostic tool to measure positions, sizes, and velocities of individual injected particles.

XFEL experiments generate large amounts of data at high rates. Preparation, execution, and data analysis of these experiments benefits from specialised software. In this work we present new open-source software tools that facilitates prediction, online-monitoring, display, and pre-processing of XFEL diffraction data.

We hope that this work is a valuable contribution in the quest of transitioning FXI from its first experimental demonstration into a technique that fulfills its potentials.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016. 84 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1451
Keyword
coherent diffractive X-ray imaging, lensless imaging, coherent X-ray diffractive imaging, flash diffractive imaging, single particle imaging, aerosol injection, electrospray injection, substrate-free sample delivery, carboxysome, phase retrieval, X-ray diffraction software, X-ray free-electron laser, XFEL, FEL, CXI, CDI, CXDI, FXI
National Category
Biophysics Atom and Molecular Physics and Optics Structural Biology
Identifiers
urn:nbn:se:uu:diva-306609 (URN)978-91-554-9748-4 (ISBN)
Public defence
2016-12-19, E10:1307-E10:1309, Biomedical Centre, Husargatan 3, Uppsala, 09:30 (English)
Opponent
Supervisors
Available from: 2016-11-29 Created: 2016-10-30 Last updated: 2016-12-28

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