Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Algorithms for Coherent Diffractive Imaging with X-ray Lasers
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.ORCID iD: 0000-0002-1887-7551
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
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. 

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2017. , p. 64
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1589
Keywords [en]
X-ray lasers, coherent diffractive imaging, algorithms, lensless imaging, flash diffractive imaging, flash X-ray imaging, aerosol injection, FEL, XFEL, CXI, CDI, FXI
National Category
Biophysics Atom and Molecular Physics and Optics
Research subject
Physics with specialization in Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-329012ISBN: 978-91-513-0129-7 (print)OAI: oai:DiVA.org:uu-329012DiVA, id: diva2:1152300
Public defence
2017-12-15, Room B7:101a, Biomedicinska Centrum (BMC), Husargatan 3, Uppsala, 13:00 (English)
Opponent
Supervisors
Available from: 2017-11-21 Created: 2017-10-24 Last updated: 2018-03-07
List of papers
1. Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
Open this publication in new window or tab >>Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
Show others...
2017 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, p. 251-262Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-323439 (URN)10.1107/S2052252517003591 (DOI)000400460500008 ()28512572 (PubMedID)
Projects
eSSENCE
Available from: 2017-04-07 Created: 2017-11-14 Last updated: 2018-04-26Bibliographically approved
2. Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time
Open this publication in new window or tab >>Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time
2016 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, p. 1042-1047Article in journal (Refereed) Published
National Category
Biophysics Software Engineering
Identifiers
urn:nbn:se:uu:diva-287197 (URN)10.1107/S1600576716005926 (DOI)000377020600036 ()
Projects
eSSENCE
Available from: 2016-04-18 Created: 2016-04-22 Last updated: 2018-01-10Bibliographically approved
3. SHARP: a distributed GPU-based ptychographic solver
Open this publication in new window or tab >>SHARP: a distributed GPU-based ptychographic solver
Show others...
2016 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, p. 1245-1252Article in journal (Refereed) Published
Abstract [en]

Ever brighter light sources, fast parallel detectors and advances in phase retrieval methods have made ptychography a practical and popular imaging technique. Compared to previous techniques, ptychography provides superior robustness and resolution at the expense of more advanced and time-consuming data analysis. By taking advantage of massively parallel architectures, high-throughput processing can expedite this analysis and provide microscopists with immediate feedback. These advances allow real-time imaging at wavelength-limited resolution, coupled with a large field of view. This article describes a set of algorithmic and computational methodologies used at the Advanced Light Source and US Department of Energy light sources. These are packaged as a CUDA-based software environment named SHARP (http://camera.lbl.gov/sharp), aimed at providing state-of-the-art high-throughput ptychography reconstructions for the coming era of diffraction-limited light sources.

Keywords
coherent X-ray diffractive imaging, ptychography, nanoscience, X-ray microscopy, phase-contrast X-ray imaging
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-300178 (URN)10.1107/S1600576716008074 (DOI)000382755900015 ()
Funder
Swedish Research CouncilSwedish Foundation for Strategic Research
Available from: 2016-08-04 Created: 2016-08-04 Last updated: 2017-10-24
4. Nanosurveyor: a framework for real-time data processing
Open this publication in new window or tab >>Nanosurveyor: a framework for real-time data processing
Show others...
2017 (English)In: Advanced Structural and Chemical Imaging, ISSN 2198-0926, Vol. 3, no 7Article in journal (Refereed) Published
Abstract [en]

Background: The ever improving brightness of accelerator based sources is enabling novel observations and discov-eries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality.

Results: Here we present an integrated software/algorithmic framework designed to capitalize on high-throughput experiments through efficient kernels, load-balanced workflows, which are scalable in design. We describe the streamlined processing pipeline of ptychography data analysis.

Conclusions: The pipeline provides throughput, compression, and resolution as well as rapid feedback to the micro-scope operators

Keywords
Streaming, Ptychography
National Category
Computer Sciences
Identifiers
urn:nbn:se:uu:diva-317013 (URN)10.1186/s40679-017-0039-0 (DOI)000411110400001 ()28261545 (PubMedID)
Funder
Swedish Research CouncilSwedish Foundation for Strategic Research
Available from: 2017-03-08 Created: 2017-03-08 Last updated: 2018-01-13Bibliographically approved
5. Wavefront sensing of individual XFEL pulses using ptychography
Open this publication in new window or tab >>Wavefront sensing of individual XFEL pulses using ptychography
Show others...
(English)Manuscript (preprint) (Other academic)
Abstract [en]

The characterization of the wavefront dynamics is important for many X-ray free-electron laser (XFEL) experiments, in particular for coherent diffractive imaging (CDI), as the reconstructed image is always the product of the incoming wavefront with the object. An accurate understanding of the wavefront is also important for any experiment wishing to achieve peak power densities, making use of the tightest possible focal spots. With the use of ptychography we demonstrate high-resolution imaging of the Linac Coherent Light Source (LCLS) beam focused at the endstation for Atomic, Molecular and Optical (AMO) experiments, including its phase and intensity at every plane along its propagation axis, for each individual pulse. Using a mixed-state approach, we have reconstructed the most dominant beam components that constitute an ensemble of pulses, and from the reconstructed components determined their respective contribution in each of the individual pulses. This enabled us to obtain complete wavefront information about each individual pulse. We hope that our findings aid interpretation of data from past and future LCLS experiments and we propose this method to be used routinely for XFEL beam diagnostics. 

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-329011 (URN)
Available from: 2017-10-24 Created: 2017-10-24 Last updated: 2017-10-24

Open Access in DiVA

fulltext(1345 kB)154 downloads
File information
File name FULLTEXT01.pdfFile size 1345 kBChecksum SHA-512
a15bee46202f350677c170b51b6b240c9209230bb30d27fd30deac3db05035ff4c2b43f347f9f07bb804edb8e490b084a219c4af89ab0ed569a1f8b494341612
Type fulltextMimetype application/pdf
Buy this publication >>

Search in DiVA

By author/editor
Daurer, Benedikt J.
By organisation
Molecular biophysics
BiophysicsAtom and Molecular Physics and Optics

Search outside of DiVA

GoogleGoogle Scholar
Total: 154 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 962 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf