Solving structure with sparse, randomly-oriented x-ray data

Philipp, Hugh T.; Ayyer, Kartik; Tate, Mark W.; Elser, Veit; Gruner, Sol M.

doi:10.1364/oe.20.013129

Solving structure with sparse, randomly-oriented x-ray data

Journal Article · Fri May 25 00:00:00 EDT 2012 · Optics Express

DOI:https://doi.org/10.1364/oe.20.013129· OSTI ID:1627125

Philipp, Hugh T. ^[1]; Ayyer, Kartik ^[2]; Tate, Mark W. ^[2]; Elser, Veit ^[2]; Gruner, Sol M. ^[3]

Cornell Univ., Ithaca, NY (United States). Lab. of Atomic and Solid State Physics; DOE/OSTI
Cornell Univ., Ithaca, NY (United States). Lab. of Atomic and Solid State Physics
Cornell Univ., Ithaca, NY (United States). Lab. of Atomic and Solid State Physics; Cornell Univ., Ithaca, NY (United States). Cornell High Energy Synchrotron Source (CHESS)

Single-particle imaging experiments of biomolecules at x-ray free-electron lasers (XFELs) require processing hundreds of thousands of images that contain very few x-rays. Each low-fluence image of the diffraction pattern is produced by a single, randomly oriented particle, such as a protein. We demonstrate the feasibility of recovering structural information at these extremes using low-fluence images of a randomly oriented 2D x-ray mask. Successful reconstruction is obtained with images averaging only 2.5 photons per frame, where it seems doubtful there could be information about the state of rotation, let alone the image contrast. This is accomplished with an expectation maximization algorithm that processes the low-fluence data in aggregate, and without any prior knowledge of the object or its orientation. The versatility of the method promises, more generally, to redefine what measurement scenarios can provide useful signal.

View Accepted Manuscript (DOE)

Research Organization:: Cornell Univ., Ithaca, NY (United States); SLAC National Accelerator Laboratory, Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)

Sponsoring Organization:: Keck Foundation; National Institute of General Medical Sciences (NIGMS); National Science Foundation (NSF); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-76SF00515; FG02-97ER62443; SC0004079; SC0005827

OSTI ID:: 1627125

Journal Information:: Optics Express, Journal Name: Optics Express Journal Issue: 12 Vol. 20; ISSN 1094-4087; ISSN OPEXFF

Publisher:: Optical Society of America (OSA)Copyright Statement

Country of Publication:: United States

Language:: English

References (20)

Potential for biomolecular imaging with femtosecond X-ray pulses Neutze, Richard; Wouts, Remco; van der Spoel, David Nature, Vol. 406, Issue 6797 https://doi.org/10.1038/35021099	journal	August 2000
High-Resolution Scanning X-ray Diffraction Microscopy Thibault, P.; Dierolf, M.; Menzel, A. Science, Vol. 321, Issue 5887 https://doi.org/10.1126/science.1158573	journal	July 2008
Cryptotomography: reconstructing 3D Fourier intensities from randomly oriented single-shot diffraction patterns Loh, N. D.; Bogan, M.; Elser, V. arXiv https://doi.org/10.48550/arxiv.1003.0846	text	January 2010
The Symmetries of Image Formation by Scattering. I. Theoretical Framework Giannakis, Dimitrios; Schwander, Peter; Ourmazd, Abbas arXiv https://doi.org/10.48550/arxiv.1009.5035	preprint	January 2010
A Mathematical Theory of Communication Shannon, C. E. Bell System Technical Journal, Vol. 27, Issue 4 https://doi.org/10.1002/j.1538-7305.1948.tb00917.x	journal	October 1948
A Mathematical Theory of Communication Shannon, C. E. Bell System Technical Journal, Vol. 27, Issue 3 https://doi.org/10.1002/j.1538-7305.1948.tb01338.x	journal	July 1948
Diffraction imaging of single particles and biomolecules Huldt, G.; Szőke, A.; Hajdu, J. Journal of Structural Biology, Vol. 144, Issue 1-2 https://doi.org/10.1016/j.jsb.2003.09.025	journal	October 2003
Energy recovery linac (ERL) coherent hard x-ray sources Bilderback, Donald H.; Brock, Joel D.; Dale, Darren S. New Journal of Physics, Vol. 12, Issue 3 https://doi.org/10.1088/1367-2630/12/3/035011	journal	March 2010
Low-flux measurements with Cornell's LCLS integrating pixel array detector Philipp, Hugh T.; Tate, Mark W.; Gruner, Sol M. Journal of Instrumentation, Vol. 6, Issue 11 https://doi.org/10.1088/1748-0221/6/11/C11006	journal	November 2011
Low-flux measurements with Cornell's LCLS integrating pixel array detector Philipp, Hugh T.; Tate, Mark W.; Gruner, Sol M. Journal of Instrumentation, Vol. 6, Issue 11 https://doi.org/10.1088/1748-0221/6/11/c11006	journal	November 2011
Reconstruction algorithm for single-particle diffraction imaging experiments Loh, Ne-Te Duane; Elser, Veit Physical Review E, Vol. 80, Issue 2 https://doi.org/10.1103/PhysRevE.80.026705	journal	August 2009
Cryptotomography: Reconstructing 3D Fourier Intensities from Randomly Oriented Single-Shot Diffraction Patterns Loh, N. D.; Bogan, M. J.; Elser, V. Physical Review Letters, Vol. 104, Issue 22 https://doi.org/10.1103/PhysRevLett.104.225501	journal	June 2010
Reconstruction algorithm for single-particle diffraction imaging experiments Loh, Ne-Te Duane; Elser, Veit Physical Review E, Vol. 80, Issue 2 https://doi.org/10.1103/physreve.80.026705	journal	August 2009
A reconstruction algorithm for single-particle diffraction imaging experiments Loh, Duane Ne-Te; Elser, Veit Acta Crystallographica Section A Foundations of Crystallography, Vol. 65, Issue a1 https://doi.org/10.1107/s0108767309098584	journal	August 2009
Graph Laplacian Tomography From Unknown Random Projections Coifman, R. R.; Shkolnisky, Y.; Sigworth, F. J. IEEE Transactions on Image Processing, Vol. 17, Issue 10 https://doi.org/10.1109/TIP.2008.2002305	journal	October 2008
Noise Limits on Reconstructing Diffraction Signals From Random Tomographs Elser, Veit IEEE Transactions on Information Theory, Vol. 55, Issue 10 https://doi.org/10.1109/TIT.2009.2027547	journal	October 2009
Graph Laplacian Tomography From Unknown Random Projections Coifman, R. R.; Shkolnisky, Y.; Sigworth, F. J. IEEE Transactions on Image Processing, Vol. 17, Issue 10 https://doi.org/10.1109/tip.2008.2002305	journal	October 2008
Noise Limits on Reconstructing Diffraction Signals From Random Tomographs Elser, Veit IEEE Transactions on Information Theory, Vol. 55, Issue 10 https://doi.org/10.1109/tit.2009.2027547	journal	October 2009
A Maximization Technique Occurring in the Statistical Analysis of Probabilistic Functions of Markov Chains Baum, Leonard E.; Petrie, Ted; Soules, George The Annals of Mathematical Statistics, Vol. 41, Issue 1 https://doi.org/10.1214/aoms/1177697196	journal	February 1970
Cryptotomography: Reconstructing 3D Fourier Intensities from Randomly Oriented Single-Shot Diffraction Patterns Loh, N. D.; Bogan, M. J.; Elser, V. Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/phppubdb-14441	text	January 2010

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Single-particle structure determination by X-ray free-electron lasers: Possibilities and challenges Hosseinizadeh, A.; Dashti, A.; Schwander, P. Structural Dynamics, Vol. 2, Issue 4 https://doi.org/10.1063/1.4919740	journal	July 2015
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Dragonfly : an implementation of the expand–maximize–compress algorithm for single-particle imaging Ayyer, Kartik; Lan, Ti-Yen; Elser, Veit Journal of Applied Crystallography, Vol. 49, Issue 4 https://doi.org/10.1107/s1600576716008165	journal	June 2016
Single-molecule imaging with longer X-ray laser pulses Martin, Andrew V.; Corso, Justine K.; Caleman, Carl IUCrJ, Vol. 2, Issue 6 https://doi.org/10.1107/s2052252515016887	journal	October 2015
Solving protein structure from sparse serial microcrystal diffraction data at a storage-ring synchrotron source Lan, Ti-Yen; Wierman, Jennifer L.; Tate, Mark W. IUCrJ, Vol. 5, Issue 5, p. 548-558 https://doi.org/10.1107/s205225251800903x	journal	July 2018
Signal-to-noise, spatial resolution and information capacity of coherent diffraction imaging Gureyev, Timur E.; Kozlov, Alexander; Nesterets, Yakov I. IUCrJ, Vol. 5, Issue 6 https://doi.org/10.1107/s2052252518010941	journal	September 2018
Experimental 3D coherent diffractive imaging from photon-sparse random projections Giewekemeyer, K.; Aquila, A.; Loh, N. -T. D. IUCrJ, Vol. 6, Issue 3 https://doi.org/10.1107/s2052252519002781	journal	March 2019
Gaussian mixture model for coarse-grained modeling from XFEL Nagai, Tetsuro; Mochizuki, Yuki; Joti, Yasumasa Optics Express, Vol. 26, Issue 20 https://doi.org/10.1364/oe.26.026734	journal	January 2018
Low-signal limit of X-ray single particle diffractive imaging Ayyer, Kartik; Morgan, Andrew J.; Aquila, Andrew Optics Express, Vol. 27, Issue 26 https://doi.org/10.1364/oe.27.037816	journal	January 2019
Experimental 3D coherent diffractive imaging from photon-sparse random projections Giewekemeyer, K.; Aquila, A.; Loh, N. -T. D. Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2019-02014	text	January 2019
Low-signal limit of X-ray single particle diffractive imaging Ayyer, Kartik; Morgan, Andrew J.; Aquila, Andrew Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2019-05177	text	January 2019

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Solving structure with sparse, randomly-oriented x-ray data Philipp, Hugh T.; Ayyer, Kartik; Tate, Mark W. https://doi.org/10.6084/m9.figshare.c.3763757 The current record is supplemented by this collection	collection	January 2012
Solving structure with sparse, randomly-oriented x-ray data Philipp, Hugh T.; Ayyer, Kartik; Tate, Mark W. https://doi.org/10.6084/m9.figshare.c.3763757.v1 The current record is supplemented by this collection	collection	January 2012

Solving structure with sparse, randomly-oriented x-ray data

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