Nanosurveyor: a framework for real-time data processing
Abstract
Background: The ever improving brightness of accelerator based sources is enabling novel observations and discoveries 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 microscope operators.
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR); Swedish Research Council (SRC); Swedish Foundation for Strategic Research (Sweden)
- OSTI Identifier:
- 1344023
- Alternate Identifier(s):
- OSTI ID: 1379699
- Grant/Contract Number:
- AC03-76SF00098; AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Advanced Structural and Chemical Imaging
- Additional Journal Information:
- Journal Name: Advanced Structural and Chemical Imaging Journal Volume: 3 Journal Issue: 1; Journal ID: ISSN 2198-0926
- Publisher:
- Springer
- Country of Publication:
- Germany
- Language:
- English
- Subject:
- 46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND TECHNOLOGY; streaming; ptychography
Citation Formats
Daurer, Benedikt J., Krishnan, Hari, Perciano, Talita, Maia, Filipe R. N. C., Shapiro, David A., Sethian, James A., and Marchesini, Stefano. Nanosurveyor: a framework for real-time data processing. Germany: N. p., 2017.
Web. doi:10.1186/s40679-017-0039-0.
Daurer, Benedikt J., Krishnan, Hari, Perciano, Talita, Maia, Filipe R. N. C., Shapiro, David A., Sethian, James A., & Marchesini, Stefano. Nanosurveyor: a framework for real-time data processing. Germany. https://doi.org/10.1186/s40679-017-0039-0
Daurer, Benedikt J., Krishnan, Hari, Perciano, Talita, Maia, Filipe R. N. C., Shapiro, David A., Sethian, James A., and Marchesini, Stefano. Tue .
"Nanosurveyor: a framework for real-time data processing". Germany. https://doi.org/10.1186/s40679-017-0039-0.
@article{osti_1344023,
title = {Nanosurveyor: a framework for real-time data processing},
author = {Daurer, Benedikt J. and Krishnan, Hari and Perciano, Talita and Maia, Filipe R. N. C. and Shapiro, David A. and Sethian, James A. and Marchesini, Stefano},
abstractNote = {Background: The ever improving brightness of accelerator based sources is enabling novel observations and discoveries 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 microscope operators.},
doi = {10.1186/s40679-017-0039-0},
journal = {Advanced Structural and Chemical Imaging},
number = 1,
volume = 3,
place = {Germany},
year = {Tue Jan 31 00:00:00 EST 2017},
month = {Tue Jan 31 00:00:00 EST 2017}
}
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Works referenced in this record:
Parallel ptychographic reconstruction
journal, January 2014
- Nashed, Youssef S. G.; Vine, David J.; Peterka, Tom
- Optics Express, Vol. 22, Issue 26
Cheetah : software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data
journal, May 2014
- Barty, Anton; Kirian, Richard A.; Maia, Filipe R. N. C.
- Journal of Applied Crystallography, Vol. 47, Issue 3
Hummingbird : monitoring and analyzing flash X-ray imaging experiments in real time
journal, April 2016
- Daurer, Benedikt J.; Hantke, Max F.; Nettelblad, Carl
- Journal of Applied Crystallography, Vol. 49, Issue 3
Ptychography and Related Diffractive Imaging Methods
book, May 2008
- Rodenburg, J. M.
- Advances in Imaging and Electron Physics
EIGER: Next generation single photon counting detector for X-ray applications
journal, September 2011
- Dinapoli, Roberto; Bergamaschi, Anna; Henrich, Beat
- Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 650, Issue 1
Ultimate upgrade for US synchrotron
journal, September 2013
- Samuel Reich, Eugenie
- Nature, Vol. 501, Issue 7466
The Coherent X-ray Imaging Data Bank
journal, August 2012
- Maia, Filipe R. N. C.
- Nature Methods, Vol. 9, Issue 9
The PILATUS 1M detector
journal, February 2006
- Broennimann, Ch.; Eikenberry, E. F.; Henrich, B.
- Journal of Synchrotron Radiation, Vol. 13, Issue 2
Development of a compact fast CCD camera and resonant soft x-ray scattering endstation for time-resolved pump-probe experiments
journal, July 2011
- Doering, D.; Chuang, Y. -D.; Andresen, N.
- Review of Scientific Instruments, Vol. 82, Issue 7
Emerging Opportunities in High-Energy X-ray Science: The Diffraction-Limited Storage Ring Frontier
journal, January 2016
- Almer, Jon; Chupas, Peter; Stephenson, Brian
- Synchrotron Radiation News, Vol. 29, Issue 1
Dask: Parallel Computation with Blocked algorithms and Task Scheduling
conference, January 2015
- Rocklin, Matthew
- Proceedings of the Python in Science Conference
Development of coherent scattering and diffractive imaging and the COSMIC facility at the Advanced Light Source
journal, March 2013
- Shapiro, D.; Roy, S.; Celestre, R.
- Journal of Physics: Conference Series, Vol. 425, Issue 19
A hard X-ray nanoprobe beamline for nanoscale microscopy
journal, September 2012
- Winarski, Robert P.; Holt, Martin V.; Rose, Volker
- Journal of Synchrotron Radiation, Vol. 19, Issue 6
High-Resolution Scanning X-ray Diffraction Microscopy
journal, July 2008
- Thibault, P.; Dierolf, M.; Menzel, A.
- Science, Vol. 321, Issue 5887
Design and performance of a scanning ptychography microscope
journal, March 2014
- Nazaretski, E.; Huang, X.; Yan, H.
- Review of Scientific Instruments, Vol. 85, Issue 3
Covalent Small Molecule Inhibitors of Ca 2+ -Bound S100B
journal, October 2014
- Cavalier, Michael C.; Pierce, Adam D.; Wilder, Paul T.
- Biochemistry, Vol. 53, Issue 42
SHARP : a distributed GPU-based ptychographic solver
journal, July 2016
- Marchesini, Stefano; Krishnan, Hari; Daurer, Benedikt J.
- Journal of Applied Crystallography, Vol. 49, Issue 4
Evidence for interstellar origin of seven dust particles collected by the Stardust spacecraft
journal, August 2014
- Westphal, A. J.; Stroud, R. M.; Bechtel, H. A.
- Science, Vol. 345, Issue 6198
A fast, direct x-ray detection charge-coupled device
journal, August 2009
- Denes, P.; Doering, D.; Padmore, H. A.
- Review of Scientific Instruments, Vol. 80, Issue 8
Hard-X-Ray Lensless Imaging of Extended Objects
journal, January 2007
- Rodenburg, J. M.; Hurst, A. C.; Cullis, A. G.
- Physical Review Letters, Vol. 98, Issue 3
The NumPy Array: A Structure for Efficient Numerical Computation
journal, March 2011
- van der Walt, Stéfan; Colbert, S. Chris; Varoquaux, Gaël
- Computing in Science & Engineering, Vol. 13, Issue 2
A computational framework for ptychographic reconstructions
journal, December 2016
- Enders, B.; Thibault, P.
- Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 472, Issue 2196
Electronic Structure of from Angle-Resolved Photoemission Spectroscopy
journal, April 2002
- Uchiyama, H.; Shen, K. M.; Lee, S.
- Physical Review Letters, Vol. 88, Issue 15
BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs
journal, March 2014
- Eklund, Anders; Dufort, Paul; Villani, Mattias
- Frontiers in Neuroinformatics, Vol. 8
The MAX IV Facility
journal, March 2013
- Eriksson, M.; Al-dmour, E.; Ahlbäck, J.
- Journal of Physics: Conference Series, Vol. 425, Issue 7