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Volume 12   Issue 2   Year 2017
Sergey A. Bobkov

Comparison Study of Different Approaches to Classification of Diffraction Images of Biological Particles Obtained in Coherent X-Ray Diffractive Imaging Experiments

Mathematical Biology & Bioinformatics. 2017;12(2):411-434.

doi: 10.17537/2017.12.411.

References

 

  1. Miao J., Ishikawa T., Johnson B., Anderson E.H., Lai B., Hodgson K.O. High resolution 3D x-ray diffraction microscopy. Physical Review Letters. 2002;89(8):088303. doi: 10.1103/PhysRevLett.89.088303
  2. Chapman H.N., Nugent K.A. Coherent lensless X-ray imaging. Nature Photonics. 2010;4(12):833-839. doi: 10.1038/nphoton.2010.240
  3. Chapman H.N., Barty A., Bogan M.J., Boutet S., Frank M., Hau-Riege S.P., Marchesini S., Woods B.W., Bajt S., Benner W.H. et al. Femtosecond diffractive imaging with a soft-X-ray free-electron laser. arXiv preprint physics/0610044. 2006.
  4. Gaffney K.J., Chapman H.N. Imaging atomic structure and dynamics with ultrafast X-ray scattering. Science. 2007;316(5830):1444-1448. doi: 10.1126/science.1135923
  5. Seibert M.M., Ekeberg T., Maia F.R., Svenda M., Andreasson J., Jonsson O., Odic D., Iwan B., Rocker A., Westphal D. et al. Single mimivirus particles intercepted and imaged with an X-ray laser. Nature. 2011;470(7332):78-81. doi: 10.1038/nature09748
  6. Mancuso A.P., Yefanov O.M., Vartanyants I.A. Coherent diffractive imaging of biological samples at synchrotron and free electron laser facilities. Journal of Biotechnology. 2010;149(4):229-237. doi: 10.1016/j.jbiotec.2010.01.024
  7. Emma P., Akre R., Arthur J., Bionta R., Bostedt C., Bozek J., Brachmann A., Bucksbaum P., Coffee R., Decker F. et al. First lasing and operation of an angstrom-wavelength free-electron laser. Nature Photonics. 2010;4(9):641-647. doi: 10.1038/nphoton.2010.176
  8. Ishikawa T., Aoyagi H., Asaka T., Asano Y., Azumi N., Bizen T., Ego H., Fukami K., Fukui T., Furukawa Y. et al. A compact X-ray free-electron laser emitting in the sub-angstrom region. Nature Photonics. 2012;6(8):540-544. doi: 10.1038/nphoton.2012.141
  9. The European X-Ray Free-Electron laser: Technical Design Report. Eds. Massimo A. et al. Hamburg, Germany: European XFEL project team, 2007.
  10. Neutze R., Wouts R., van der Spoel D., Weckert E., Hajdu J. Potential for biomolecular imaging with femtosecond X-ray pulses. Nature. 2000;406(6797):752-757. doi: 10.1038/35021099
  11. Lorenz U., Kabachnik N.M., Weckert E., Vartanyants I.A. Impact of ultrafast electronic damage in single-particle x-ray imaging experiments. Physical Review E. 2012;86(5):051911. doi: 10.1103/PhysRevE.86.051911
  12. Gorobtsov O.Y., Lorenz U., Kabachnik N.M., Vartanyants I.A. 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. Physical Review E. 2015;91(6):062712. doi: 10.1103/PhysRevE.91.062712
  13. Ne-Te Duane Loh, Veit Elser. Reconstruction algorithm for single-particle diffraction imaging experiments. Physical Review E. 2009;80(2).
  14. Fienup J.R. Reconstruction of an object from the modulus of its Fourier transform. Optics Letters. 1978;3(1):27-29. doi: 10.1364/OL.3.000027
  15. Fienup J.R. Phase retrieval algorithms: a comparison. Appl. Opt. 1982;21(15):2758. doi: 10.1364/AO.21.002758
  16. Chen C., Miao J., Wang C., Lee T. Application of optimization technique to noncrystalline x-ray diffraction microscopy: Guided hybrid input-output method. Physical Review B. 2007;76(6):064113. doi: 10.1103/PhysRevB.76.064113
  17. Yoon C.H., Schwander P., Abergel C., Andersson I., Andreasson J., Aquila A., Bajt S., Barthelmess M., Barty A., Bogan M.J. et al. Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering. Optics Express. 2011;19(17):16542-16549. doi: 10.1364/OE.19.016542
  18. Bobkov S.A., Teslyuk A.B., Kurta R.P., Gorobtsov O.Y., Yefanov O.M., Ilyin V.A., Senin R.A., Vartanyants I.A. Sorting algorithms for single-particle imaging experiments at X-ray free-electron lasers. Journal of Synchrotron Radiation. 2015;22:1345-1352. doi: 10.1107/S1600577515017348
  19. Bobkov S.A., Teslyuk A.B., Ilyin V.A., Vartanyants I.A. Diffraction images classification for biological particles with different symmetry types in coherent X-ray Diffraction Imaging Experiments. Mathematical Biology and Bioinformatics . 2016;11(2):299-310. doi: 10.17537/2016.11.299
  20. Maia F.R.N.C. The Coherent X-ray Imaging Data Bank. Nature Methods. 2012;9(9):854-855. doi: 10.1038/nmeth.2110
  21. Struder L., Epp S., Rolles D., Hartmann R., Holl P., Lutz G., Soltau H., Eckart R., Reich C., Heinzinger K. 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. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 2010;614(3):483-496. doi: 10.1016/j.nima.2009.12.053
  22. Kassemeyer S., Steinbrener J., Lomb L., Hartmann E., Aquila A., Barty A., Martin A.V., Hampton C.Y., Bajt S., Barthelmess M. et al. Femtosecond free-electron laser x-ray diffraction data sets for algorithm development. Optics Express. 2012;20(4):4149-4158. doi: 10.1364/OE.20.004149
  23. Van Etten J.L., Burbank D.E., Xia Y., Meints R.H. Growth cycle of a virus, PBCV-1, that infects Chlorella-like algae. Virology. 1983;126(1):117-125. doi: 10.1016/0042-6822(83)90466-X
  24. Starodub D., Aquila A., Bajt S., Barthelmess M., Barty A., Bostedt C., Bozek J.D., Coppola N., Doak R.B., Epp S.W. et al. Single-particle structure determination by correlations of snapshot X-ray diffraction patterns. Nature Communications. 2012;3:1276. doi: 10.1038/ncomms2288
  25. Hantke M.F., Hasse D., Maia F.R., Ekeberg T., John K., Svenda M., Loh N.D., Martin A.V., Timneanu N., Larsson D.S. et al. High-throughput imaging of heterogeneous cell organelles with an X-ray laser. Nature Photonics. 2014;8(12):943-949. doi: 10.1038/nphoton.2014.270
  26. Van Der Schot G., Svenda M., Maia F.R., Hantke M.F., DePonte D.P., Seibert M.M., Aquila A., Schulz J., Kirian R.A., Liang M. et al. Open data set of live cyanobacterial cells imaged using an X-ray laser. Scientific Data. 2016;3. doi: 10.1038/sdata.2016.58
  27. Ting K.M. Precision and Recall. In: Encyclopedia of Machine Learning. Springer; 2010. 781 p. ISBN 978-0-387-30164-8.
  28. Cortes C., Vapnik V. Support-vector networks. Machine Learning. 1995;20(3):273-297. doi: 10.1007/BF00994018
  29. Rosenblatt F. Principles of neurodynamics. Perceptrons and the theory of brain mechanisms. 1961.
  30. LeCun Y., Bengio Y., Hinton G. Deep learning. Nature. 2015;521(7553):436-444. doi: 10.1038/nature14539
  31. Henrich B., Becker J., Dinapoli R., Goettlicher P., Graafsma H., Hirsemann H., Klanner R., Krueger H., Mazzocco R., Mozzanica A. et al. The adaptive gain integrating pixel detector AGIPD a detector for the European XFEL. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 2011;633:S11-S14. doi: 10.1016/j.nima.2010.06.107
  32. Fisher R.A. The use of multiple measurements in taxonomic problems. Annals of Human Genetics. 1936;7(2):179-188. doi: 10.1111/j.1469-1809.1936.tb02137.x
  33. Cover T.M. Geometrical and statistical properties of systems of linear inequalities with applications in pattern recognition. IEEE Transactions on Electronic Computers. 1965;3:326-334. doi: 10.1109/PGEC.1965.264137
  34. Steinhaus H. Sur la division des corp materiels en parties. Bull. Acad. Polon. Sci. 1956;1(804):801.
  35. Lloyd S. Least squares quantization in PCM. IEEE Transactions on Information Theory. 1982;28(2):129-137. doi: 10.1109/TIT.1982.1056489
  36. Shi J., Malik J. Normalized cuts and image segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2000;22(8):888-905. doi: 10.1109/34.868688
  37. Ward Jr J.H. Hierarchical grouping to optimize an objective function. Journal of the American Statistical Association. 1963;58(301):236-244. doi: 10.1080/01621459.1963.10500845
  38. Zhang T., Ramakrishnan R., Livny M. BIRCH: an efficient data clustering method for very large databases. In: Proceeding SIGMOD '96 Proceedings of the 1996 ACM SIGMOD international conference on Management of data. 1996;25(2):103-114. doi: 10.1145/233269.233324
  39. Cheng Y. Mean shift, mode seeking, and clustering. IEEE Transactions on Pattern Analysis and Machine Intelligence. 1995;17(8):790-799. doi: 10.1109/34.400568
  40. Frey B.J., Dueck D. Clustering by passing messages between data points. Science. 2007;315(5814):972-976. doi: 10.1126/science.1136800
  41. Ester M., Kriegel H., Sander J., Xu X. A density-based algorithm for discovering clusters in large spatial databases with noise. In: KDD-96 Proceedings. 1996;96(34):226-231.
  42. Hahnloser R.H.R., Sarpeshkar R., Mahowald M.A., Douglas R.J., Seung H.S. Digital selection and analogue amplification coexist in a cortex-inspired silicon circuit. Nature. 2000;405(6789):947-951. doi: 10.1038/35016072
  43. Bishop C.M. Pattern recognition and machine learning. 2006.
  44. Hinton G.E., Srivastava N., Krizhevsky A., Sutskever I., Salakhutdinov R.R. Improving neural networks by preventing co-adaptation of feature detectors. arXiv preprint arXiv:1207.0580. 2012.
  45. Altarelli M., Kurta R.P., Vartanyants I.A. X-ray cross-correlation analysis and local symmetries of disordered systems: General theory. Physical Review B. 2010;82(10):104207. doi: 10.1103/PhysRevB.82.104207
  46. Kurta R.P., Dronyak R., Altarelli M., Weckert E., Vartanyants I.A. Solution of the phase problem for coherent scattering from a disordered system of identical particles. New Journal of Physics. 2013;15(1):013059. doi: 10.1088/1367-2630/15/1/013059
  47. Pedrini B., Menzel A., Guizar-Sicairos M., Guzenko V., Gorelick S., David C., Patterson B.D., Abela R. Two-dimensional structure from random multiparticle X-ray scattering images using cross-correlations. Nature Communications. 2013;4:1647. doi: 10.1038/ncomms2622
  48. Saldin D.K., Poon H., Schwander P., Uddin M., Schmidt M. Reconstructing an icosahedral virus from single-particle diffraction experiments. Optics Express. 2011;19(18):17318-17335. doi: 10.1364/OE.19.017318
Table of Contents Original Article
Math. Biol. Bioinf.
2017;12(2):411-434
doi: 10.17537/2017.12.411
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

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