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Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time
Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.ORCID-id: 0000-0002-1887-7551
Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.ORCID-id: 0000-0003-1251-0465
Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap. Uppsala universitet, Science for Life Laboratory, SciLifeLab.ORCID-id: 0000-0003-0458-6902
Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
2016 (engelsk)Inngår i: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, s. 1042-1047Artikkel i tidsskrift (Fagfellevurdert) Published
Resurstyp
Text
sted, utgiver, år, opplag, sider
2016. Vol. 49, s. 1042-1047
HSV kategori
Identifikatorer
URN: urn:nbn:se:uu:diva-287197DOI: 10.1107/S1600576716005926ISI: 000377020600036OAI: oai:DiVA.org:uu-287197DiVA, id: diva2:922323
Prosjekter
eSSENCETilgjengelig fra: 2016-04-18 Laget: 2016-04-22 Sist oppdatert: 2018-01-10bibliografisk kontrollert
Inngår i avhandling
1. Coherent Diffractive Imaging with X-ray Lasers
Åpne denne publikasjonen i ny fane eller vindu >>Coherent Diffractive Imaging with X-ray Lasers
2016 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
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.

sted, utgiver, år, opplag, sider
Uppsala: Acta Universitatis Upsaliensis, 2016. s. 84
Serie
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1451
Emneord
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
HSV kategori
Identifikatorer
urn:nbn:se:uu:diva-306609 (URN)978-91-554-9748-4 (ISBN)
Disputas
2016-12-19, E10:1307-E10:1309, Biomedical Centre, Husargatan 3, Uppsala, 09:30 (engelsk)
Opponent
Veileder
Tilgjengelig fra: 2016-11-29 Laget: 2016-10-30 Sist oppdatert: 2016-12-28
2. Algorithms for Coherent Diffractive Imaging with X-ray Lasers
Åpne denne publikasjonen i ny fane eller vindu >>Algorithms for Coherent Diffractive Imaging with X-ray Lasers
2017 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
Abstract [en]

Coherent diffractive imaging (CDI) has become a very popular technique over the past two decades. CDI is a "lensless" imaging method which replaces the objective lens of a conventional microscope by a computational image reconstruction procedure. Its increase in popularity came together with the development of X-ray free-electron lasers (XFELs) which produce extremely bright and coherent X-rays. By facilitating these unique properties, CDI enables structure determination of non-crystalline samples at nanometre resolution and has many applications in structural biology, material science and X-ray optics among others. This work focuses on two specific CDI techniques, flash X-ray diffractive imaging (FXI) on biological samples and X-ray ptychography.

While the first FXI demonstrations using soft X-rays have been quite promising, they also revealed remaining technical challenges. FXI becomes even more demanding when approaching shorter wavelengths to allow subnanometre resolution imaging. We described one of the first FXI experiments using hard X-rays and characterized the most critical components of such an experiment, namely the properties of X-ray focus, sample delivery and detectors. Based on our findings, we discussed experimental and computational strategies for FXI to overcome its current difficulties and reach its full potential. We deposited the data in the Coherent X-ray Database (CXIDB) and made our data analysis code available in a public repository. We developed algorithms targeted towards the needs of FXI experiments and implemented a software package which enables the analysis of diffraction data in real time.

X-ray ptychography has developed into a very useful tool for quantitative imaging of complex materials and has found applications in many areas. However, it involves a computational reconstruction step which can be slow. Therefore, we developed a fast GPU-based ptychographic solver and combined it with a framework for real-time data processing which already starts the ptychographic reconstruction process while data is still being collected. This provides immediate feedback to the user and allows high-throughput ptychographic imaging.

Finally, we have used ptychographic imaging as a method to study the wavefront of a focused XFEL beam under typical FXI conditions. 

We are convinced that this work on developing strategies and algorithms for FXI and ptychography is a valuable contribution to the development of coherent diffractive imaging. 

sted, utgiver, år, opplag, sider
Uppsala: Acta Universitatis Upsaliensis, 2017. s. 64
Serie
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1589
Emneord
X-ray lasers, coherent diffractive imaging, algorithms, lensless imaging, flash diffractive imaging, flash X-ray imaging, aerosol injection, FEL, XFEL, CXI, CDI, FXI
HSV kategori
Forskningsprogram
Fysik med inriktning mot biofysik
Identifikatorer
urn:nbn:se:uu:diva-329012 (URN)978-91-513-0129-7 (ISBN)
Disputas
2017-12-15, Room B7:101a, Biomedicinska Centrum (BMC), Husargatan 3, Uppsala, 13:00 (engelsk)
Opponent
Veileder
Tilgjengelig fra: 2017-11-21 Laget: 2017-10-24 Sist oppdatert: 2018-03-07

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