A convolutional neural network-based screening tool for X-ray serial crystallography

Ke, Tsung-Wei; Brewster, Aaron S.; Yu, Stella X.; Ushizima, Daniela; Yang, Chao; Sauter, Nicholas K.

doi:10.1107/S1600577518004873

A convolutional neural network-based screening tool for X-ray serial crystallography

Journal Article · Tue Apr 24 00:00:00 EDT 2018 · Journal of Synchrotron Radiation (Online)

DOI:https://doi.org/10.1107/S1600577518004873· OSTI ID:1434392

Ke, Tsung-Wei; Brewster, Aaron S.; Yu, Stella X.; Ushizima, Daniela; Yang, Chao; Sauter, Nicholas K.

A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231; AC02-76SF00515

OSTI ID:: 1434392

Alternate ID(s):: OSTI ID: 22735907
OSTI ID: 1460313

Journal Information:: Journal of Synchrotron Radiation (Online), Journal Name: Journal of Synchrotron Radiation (Online) Journal Issue: 3 Vol. 25; ISSN 1600-5775; ISSN JSYRES

Publisher:: International Union of Crystallography (IUCr)Copyright Statement

Country of Publication:: Denmark

Language:: English

References (31)

The crystal structure of an oxygen-tolerant hydrogenase uncovers a novel iron-sulphur centre Fritsch, Johannes; Scheerer, Patrick; Frielingsdorf, Stefan Nature, Vol. 479, Issue 7372 https://doi.org/10.1038/nature10505	journal	October 2011
Deep learning LeCun, Yann; Bengio, Yoshua; Hinton, Geoffrey Nature, Vol. 521, Issue 7553 https://doi.org/10.1038/nature14539	journal	May 2015
Structure of photosystem II and substrate binding at room temperature Young, Iris D.; Ibrahim, Mohamed; Chatterjee, Ruchira Nature, Vol. 540, Issue 7633 https://doi.org/10.1038/nature20161	journal	November 2016
Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography Weierstall, Uwe; James, Daniel; Wang, Chong Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms4309	journal	February 2014
The Coherent X-ray Imaging Data Bank Maia, Filipe R. N. C. Nature Methods, Vol. 9, Issue 9 https://doi.org/10.1038/nmeth.2110	journal	August 2012
Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers Hattne, Johan; Echols, Nathaniel; Tran, Rosalie Nature Methods, Vol. 11, Issue 5 https://doi.org/10.1038/nmeth.2887	journal	March 2014
Grease matrix as a versatile carrier of proteins for serial crystallography Sugahara, Michihiro; Mizohata, Eiichi; Nango, Eriko Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3172	journal	November 2014
Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II Sierra, Raymond G.; Gati, Cornelius; Laksmono, Hartawan Nature Methods, Vol. 13, Issue 1 https://doi.org/10.1038/nmeth.3667	journal	November 2015
Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers Fuller, Franklin D.; Gul, Sheraz; Chatterjee, Ruchira Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4195	journal	February 2017
High-speed fixed-target serial virus crystallography Roedig, Philip; Ginn, Helen M.; Pakendorf, Tim Nature Methods, Vol. 14, Issue 8 https://doi.org/10.1038/nmeth.4335	journal	June 2017
Injector for scattering measurements on fully solvated biospecies Weierstall, U.; Spence, J. C. H.; Doak, R. B. Review of Scientific Instruments, Vol. 83, Issue 3 https://doi.org/10.1063/1.3693040	journal	March 2012
Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode Alonso-Mori, R.; Kern, J.; Gildea, R. J. Proceedings of the National Academy of Sciences, Vol. 109, Issue 47, p. 19103-19107 https://doi.org/10.1073/pnas.1211384109	journal	November 2012
Convolutional networks for fast, energy-efficient neuromorphic computing Esser, Steven K.; Merolla, Paul A.; Arthur, John V. Proceedings of the National Academy of Sciences, Vol. 113, Issue 41 https://doi.org/10.1073/pnas.1604850113	journal	September 2016
The New Macromolecular Femtosecond Crystallography (MFX) Instrument at LCLS Boutet, Sébastien; Cohen, Aina E.; Wakatsuki, Soichi Synchrotron Radiation News, Vol. 29, Issue 1 https://doi.org/10.1080/08940886.2016.1124681	journal	January 2016
CSPAD upgrades and CSPAD V1.5 at LCLS Herrmann, S.; Hart, P.; Dragone, A. Journal of Physics: Conference Series, Vol. 493 https://doi.org/10.1088/1742-6596/493/1/012013	journal	March 2014
Automated diffraction image analysis and spot searching for high-throughput crystal screening Zhang, Zepu; Sauter, Nicholas K.; van den Bedem, Henry Journal of Applied Crystallography, Vol. 39, Issue 1 https://doi.org/10.1107/S0021889805040677	journal	January 2006
Nanoflow electrospinning serial femtosecond crystallography Sierra, Raymond G.; Laksmono, Hartawan; Kern, Jan Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 11, p. 1584-1587 https://doi.org/10.1107/S0907444912038152	journal	October 2012
New Python-based methods for data processing Sauter, Nicholas K.; Hattne, Johan; Grosse-Kunstleve, Ralf W. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000863	journal	June 2013
Application of a neural network in high-throughput protein crystallography Berntson, A.; Stojanoff, V.; Takai, H. Journal of Synchrotron Radiation, Vol. 10, Issue 6 https://doi.org/10.1107/S0909049503020855	journal	October 2003
The point-spread function of fiber-coupled area detectors Holton, James M.; Nielsen, Chris; Frankel, Kenneth A. Journal of Synchrotron Radiation, Vol. 19, Issue 6 https://doi.org/10.1107/S0909049512035571	journal	September 2012
Cheetah : software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data Barty, Anton; Kirian, Richard A.; Maia, Filipe R. N. C. Journal of Applied Crystallography, Vol. 47, Issue 3 https://doi.org/10.1107/S1600576714007626	journal	May 2014
IOTA : integration optimization, triage and analysis tool for the processing of XFEL diffraction images Lyubimov, Artem Y.; Uervirojnangkoorn, Monarin; Zeldin, Oliver B. Journal of Applied Crystallography, Vol. 49, Issue 3 https://doi.org/10.1107/S1600576716006683	journal	May 2016
Data systems for the Linac Coherent Light Source Thayer, J.; Damiani, D.; Ford, C. Journal of Applied Crystallography, Vol. 49, Issue 4 https://doi.org/10.1107/S1600576716011055	journal	July 2016
The Coherent X-ray Imaging instrument at the Linac Coherent Light Source Liang, Mengning; Williams, Garth J.; Messerschmidt, Marc Journal of Synchrotron Radiation, Vol. 22, Issue 3 https://doi.org/10.1107/S160057751500449X	journal	April 2015
The Linac Coherent Light Source White, William E.; Robert, Aymeric; Dunne, Mike Journal of Synchrotron Radiation, Vol. 22, Issue 3 https://doi.org/10.1107/S1600577515005196	journal	April 2015
X-ray detectors at the Linac Coherent Light Source Blaj, Gabriel; Caragiulo, Pietro; Carini, Gabriella Journal of Synchrotron Radiation, Vol. 22, Issue 3 https://doi.org/10.1107/S1600577515005317	journal	April 2015
A convolutional neural network approach to calibrating the rotation axis for X-ray computed tomography Yang, Xiaogang; De Carlo, Francesco; Phatak, Charudatta Journal of Synchrotron Radiation, Vol. 24, Issue 2 https://doi.org/10.1107/S1600577516020117	journal	January 2017
DIALS : implementation and evaluation of a new integration package Winter, Graeme; Waterman, David G.; Parkhurst, James M. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 2 https://doi.org/10.1107/S2059798317017235	journal	February 2018
The CSPAD megapixel x-ray camera at LCLS Hart, Philip; Boutet, Sébastien; Carini, Gabriella SPIE Optical Engineering + Applications, SPIE Proceedings https://doi.org/10.1117/12.930924	conference	October 2012
A million spiking-neuron integrated circuit with a scalable communication network and interface Merolla, P. A.; Arthur, J. V.; Alvarez-Icaza, R. Science, Vol. 345, Issue 6197 https://doi.org/10.1126/science.1254642	journal	August 2014
Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography Keedy, Daniel A.; Kenner, Lillian R.; Warkentin, Matthew eLife, Vol. 4 https://doi.org/10.7554/eLife.07574	journal	September 2015

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