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Nanosurveyor: a framework for real-time data processing
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.ORCID iD: 0000-0002-1887-7551
Lawrence Berkeley National Laboratory, Computational Research Division.
Lawrence Berkeley National Laboratory, Computational Research Division.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Lawrence Berkeley National Laboratory, NERSC.
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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

Place, publisher, year, edition, pages
2017. Vol. 3, no 7
Keyword [en]
Streaming, Ptychography
National Category
Computer Science
Identifiers
URN: urn:nbn:se:uu:diva-317013DOI: 10.1186/s40679-017-0039-0ISI: 000411110400001PubMedID: 28261545OAI: oai:DiVA.org:uu-317013DiVA: diva2:1079596
Funder
Swedish Research CouncilSwedish Foundation for Strategic Research
Available from: 2017-03-08 Created: 2017-03-08 Last updated: 2017-12-08Bibliographically approved
In thesis
1. Algorithms for Coherent Diffractive Imaging with X-ray Lasers
Open this publication in new window or tab >>Algorithms for Coherent Diffractive Imaging with X-ray Lasers
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. 64 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1589
Keyword
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:nbn:se:uu:diva-329012 (URN)978-91-513-0129-7 (ISBN)
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: 2017-11-21

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Daurer, Benedikt J.Rocha Neves Couto Maia, Filipe

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