Sorting algorithms for single-particle imaging experiments at X-ray free-electron lasers.

Modern X-ray free-electron lasers (XFELs) operating at high repetition rates produce a tremendous amount of data. It is a great challenge to classify this information and reduce the initial data set to a manageable size for further analysis. Here an approach for classification of diffraction patterns measured in prototypical diffract-and-destroy single-particle imaging experiments at XFELs is presented. It is proposed that the data are classified on the basis of a set of parameters that take into account the underlying diffraction physics and specific relations between the real-space structure of a particle and its reciprocal-space intensity distribution. The approach is demonstrated by applying principal component analysis and support vector machine algorithms to the simulated and measured X-ray data sets.

[1]  J. Drenth Principles of protein x-ray crystallography , 1994 .

[2]  D. Stuart,et al.  The atomic structure of the bluetongue virus core , 1998, Nature.

[3]  Garth J. Williams,et al.  Single mimivirus particles intercepted and imaged with an X-ray laser , 2011, Nature.

[4]  H. N. Chapman,et al.  Imaging Atomic Structure and Dynamics with Ultrafast X-ray Scattering , 2007, Science.

[5]  Garth J. Williams,et al.  High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography , 2012, Science.

[6]  M. Schmidt,et al.  Reconstructing an icosahedral virus from single-particle diffraction experiments. , 2011, Optics express.

[7]  R. Feidenhansl The European X-ray Free-Electron Laser , 2017 .

[8]  J. Hajdu,et al.  Potential for biomolecular imaging with femtosecond X-ray pulses , 2000, Nature.

[9]  A. H. Walenta,et al.  Large-format, high-speed, X-ray pnCCDs combined with electron and ion imaging spectrometers in a multipurpose chamber for experiments at 4th generation light sources , 2010 .

[10]  J. Als-Nielsen,et al.  Elements of Modern X-ray Physics: Als-Nielsen/Elements , 2011 .

[11]  Alexander J. Smola,et al.  Advances in Large Margin Classifiers , 2000 .

[12]  R. Santra,et al.  The linac coherent light source single particle imaging road map , 2015, Structural dynamics.

[13]  T. Ishikawa,et al.  A compact X-ray free-electron laser emitting in the sub-ångström region , 2012, Nature Photonics.

[14]  Heng Tao Shen,et al.  Principal Component Analysis , 2009, Encyclopedia of Biometrics.

[15]  J. Bozek AMO instrumentation for the LCLS X-ray FEL , 2009 .

[16]  E. Weckert,et al.  Impact of ultrafast electronic damage in single-particle x-ray imaging experiments. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[17]  A. Ourmazd,et al.  Structure from Fleeting Illumination of Faint Spinning Objects in Flight with Application to Single Molecules , 2008, 0806.2341.

[18]  Georg Weidenspointner,et al.  Femtosecond free-electron laser x-ray diffraction data sets for algorithm development. , 2011, Optics express.

[19]  Corinna Cortes,et al.  Support-Vector Networks , 1995, Machine Learning.

[20]  F. Maia The Coherent X-ray Imaging Data Bank , 2012, Nature Methods.

[21]  Anton Barty,et al.  High-throughput imaging of heterogeneous cell organelles with an X-ray laser , 2014, Nature Photonics.

[22]  C. David,et al.  Two-dimensional structure from random multiparticle X-ray scattering images using cross-correlations , 2013, Nature Communications.

[23]  Georg Weidenspointner,et al.  Femtosecond X-ray protein nanocrystallography , 2011, Nature.

[24]  Alejandro F. Frangi,et al.  Two-dimensional PCA: a new approach to appearance-based face representation and recognition , 2004 .

[25]  S. Cusack,et al.  Structural and biochemical characterization of a human adenovirus 2/12 penton base chimera , 2006, The FEBS journal.

[26]  Pavel Berkhin,et al.  A Survey of Clustering Data Mining Techniques , 2006, Grouping Multidimensional Data.

[27]  E. Weckert,et al.  Cross-correlation analysis of x-ray scattering from oxygen clusters , 2013 .

[28]  Marc Teboulle,et al.  Grouping Multidimensional Data - Recent Advances in Clustering , 2006 .

[29]  D. Ratner,et al.  First lasing and operation of an ångstrom-wavelength free-electron laser , 2010 .

[30]  E. Weckert,et al.  X-ray cross-correlation analysis applied to disordered two-dimensional systems , 2012, 1202.6253.

[31]  Veit Elser,et al.  Reconstruction algorithm for single-particle diffraction imaging experiments. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

[32]  Z. Kam Determination of Macromolecular Structure in Solution by Spatial Correlation of Scattering Fluctuations , 1977 .

[33]  I. A. Vartanyants,et al.  Orientation determination in single-particle x-ray coherent diffraction imaging experiments , 2013, 1302.5730.

[34]  E. Weckert,et al.  Solution of the phase problem for coherent scattering from a disordered system of identical particles , 2012, 1210.3519.

[35]  Andrew V. Martin,et al.  Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering. , 2011, Optics express.

[36]  O Yu Gorobtsov,et al.  Theoretical study of electronic damage in single-particle imaging experiments at x-ray free-electron lasers for pulse durations from 0.1 to 10 fs. , 2015, Physical review. E, Statistical, nonlinear, and soft matter physics.

[37]  I. Vartanyants,et al.  X-Ray Cross-Correlation Analysis of Disordered Ensembles of Particles: Potentials and Limitations , 2013, 1302.5805.

[38]  Anton Barty,et al.  Automated identification and classification of single particle serial femtosecond X-ray diffraction data. , 2014, Optics express.

[39]  Christian Gutt,et al.  X-ray cross correlation analysis uncovers hidden local symmetries in disordered matter , 2009, Proceedings of the National Academy of Sciences.

[40]  R. Henderson The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules , 1995, Quarterly Reviews of Biophysics.

[41]  J. V. Van Etten,et al.  Growth cycle of a virus, PBCV-1, that infects Chlorella-like algae. , 1983, Virology.

[42]  O M Yefanov,et al.  Coherent diffractive imaging of biological samples at synchrotron and free electron laser facilities. , 2010, Journal of biotechnology.

[43]  J. Kirz,et al.  An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy. , 2005, Journal of Electron Spectroscopy and Related Phenomena.

[44]  Gianluca Geloni,et al.  The European X-ray Free-Electron Laser , 2015 .

[45]  Fabrizio Sebastiani,et al.  Machine learning in automated text categorization , 2001, CSUR.