Literature DB >> 21935018

Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering.

Chun Hong Yoon1, Peter Schwander, Chantal Abergel, Inger Andersson, Jakob Andreasson, Andrew Aquila, Saša Bajt, Miriam Barthelmess, Anton Barty, Michael J Bogan, Christoph Bostedt, John Bozek, Henry N Chapman, Jean-Michel Claverie, Nicola Coppola, Daniel P DePonte, Tomas Ekeberg, Sascha W Epp, Benjamin Erk, Holger Fleckenstein, Lutz Foucar, Heinz Graafsma, Lars Gumprecht, Janos Hajdu, Christina Y Hampton, Andreas Hartmann, Elisabeth Hartmann, Robert Hartmann, Gunter Hauser, Helmut Hirsemann, Peter Holl, Stephan Kassemeyer, Nils Kimmel, Maya Kiskinova, Mengning Liang, Ne-Te Duane Loh, Lukas Lomb, Filipe R N C Maia, Andrew V Martin, Karol Nass, Emanuele Pedersoli, Christian Reich, Daniel Rolles, Benedikt Rudek, Artem Rudenko, Ilme Schlichting, Joachim Schulz, Marvin Seibert, Virginie Seltzer, Robert L Shoeman, Raymond G Sierra, Heike Soltau, Dmitri Starodub, Jan Steinbrener, Gunter Stier, Lothar Strüder, Martin Svenda, Joachim Ullrich, Georg Weidenspointner, Thomas A White, Cornelia Wunderer, Abbas Ourmazd.   

Abstract

Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.
© 2011 Optical Society of America

Year:  2011        PMID: 21935018     DOI: 10.1364/OE.19.016542

Source DB:  PubMed          Journal:  Opt Express        ISSN: 1094-4087            Impact factor:   3.894


  19 in total

1.  Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase.

Authors:  Jeffrey J Donatelli; James A Sethian; Peter H Zwart
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-26       Impact factor: 11.205

Review 2.  Methods and application of coherent X-ray diffraction imaging of noncrystalline particles.

Authors:  Masayoshi Nakasako; Amane Kobayashi; Yuki Takayama; Kenta Asakura; Mao Oide; Koji Okajima; Tomotaka Oroguchi; Masaki Yamamoto
Journal:  Biophys Rev       Date:  2020-03-16

Review 3.  Emerging opportunities in structural biology with X-ray free-electron lasers.

Authors:  Ilme Schlichting; Jianwei Miao
Journal:  Curr Opin Struct Biol       Date:  2012-08-22       Impact factor: 6.809

4.  Data processing software suite SITENNO for coherent X-ray diffraction imaging using the X-ray free-electron laser SACLA.

Authors:  Yuki Sekiguchi; Tomotaka Oroguchi; Yuki Takayama; Masayoshi Nakasako
Journal:  J Synchrotron Radiat       Date:  2014-03-15       Impact factor: 2.616

Review 5.  Conformations of macromolecules and their complexes from heterogeneous datasets.

Authors:  P Schwander; R Fung; A Ourmazd
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-07-17       Impact factor: 6.237

6.  Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data.

Authors:  Anton Barty; Richard A Kirian; Filipe R N C Maia; Max Hantke; Chun Hong Yoon; Thomas A White; Henry Chapman
Journal:  J Appl Crystallogr       Date:  2014-05-29       Impact factor: 3.304

7.  Data acquisition system for X-ray free-electron laser experiments at SACLA.

Authors:  Yasumasa Joti; Takashi Kameshima; Mitsuhiro Yamaga; Takashi Sugimoto; Kensuke Okada; Toshinori Abe; Yukito Furukawa; Toru Ohata; Ryotaro Tanaka; Takaki Hatsui; Makina Yabashi
Journal:  J Synchrotron Radiat       Date:  2015-04-17       Impact factor: 2.616

8.  Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser.

Authors:  Tomas Ekeberg; Martin Svenda; M Marvin Seibert; Chantal Abergel; Filipe R N C Maia; Virginie Seltzer; Daniel P DePonte; Andrew Aquila; Jakob Andreasson; Bianca Iwan; Olof Jönsson; Daniel Westphal; Duško Odić; Inger Andersson; Anton Barty; Meng Liang; Andrew V Martin; Lars Gumprecht; Holger Fleckenstein; Saša Bajt; Miriam Barthelmess; Nicola Coppola; Jean-Michel Claverie; N Duane Loh; Christoph Bostedt; John D Bozek; Jacek Krzywinski; Marc Messerschmidt; Michael J Bogan; Christina Y Hampton; Raymond G Sierra; Matthias Frank; Robert L Shoeman; Lukas Lomb; Lutz Foucar; Sascha W Epp; Daniel Rolles; Artem Rudenko; Robert Hartmann; Andreas Hartmann; Nils Kimmel; Peter Holl; Georg Weidenspointner; Benedikt Rudek; Benjamin Erk; Stephan Kassemeyer; Ilme Schlichting; Lothar Strüder; Joachim Ullrich; Carlo Schmidt; Faton Krasniqi; Günter Hauser; Christian Reich; Heike Soltau; Sebastian Schorb; Helmut Hirsemann; Cornelia Wunderer; Heinz Graafsma; Henry Chapman; Janos Hajdu
Journal:  Sci Data       Date:  2016-08-01       Impact factor: 6.444

9.  Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses.

Authors:  Ruslan P Kurta; Jeffrey J Donatelli; Chun Hong Yoon; Peter Berntsen; Johan Bielecki; Benedikt J Daurer; Hasan DeMirci; Petra Fromme; Max Felix Hantke; Filipe R N C Maia; Anna Munke; Carl Nettelblad; Kanupriya Pande; Hemanth K N Reddy; Jonas A Sellberg; Raymond G Sierra; Martin Svenda; Gijs van der Schot; Ivan A Vartanyants; Garth J Williams; P Lourdu Xavier; Andrew Aquila; Peter H Zwart; Adrian P Mancuso
Journal:  Phys Rev Lett       Date:  2017-10-12       Impact factor: 9.161

10.  High-resolution structure of viruses from random diffraction snapshots.

Authors:  A Hosseinizadeh; P Schwander; A Dashti; R Fung; R M D'Souza; A Ourmazd
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-07-17       Impact factor: 6.237

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