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Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data
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.
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2014 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 47, 1118-1131 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2014. Vol. 47, 1118-1131 p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-228011DOI: 10.1107/S1600576714007626ISI: 000336738500032OAI: oai:DiVA.org:uu-228011DiVA: diva2:731994
Available from: 2014-07-03 Created: 2014-07-02 Last updated: 2017-12-05Bibliographically 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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