Literature DB >> 33441629

An encryption-decryption framework to validating single-particle imaging.

Zhou Shen1,2, Colin Zhi Wei Teo1,2, Kartik Ayyer3,4, N Duane Loh5,6,7.   

Abstract

We propose an encryption-decryption framework for validating diffraction intensity volumes reconstructed using single-particle imaging (SPI) with X-ray free-electron lasers (XFELs) when the ground truth volume is absent. This conceptual framework exploits each reconstructed volumes' ability to decipher latent variables (e.g. orientations) of unseen sentinel diffraction patterns. Using this framework, we quantify novel measures of orientation disconcurrence, inconsistency, and disagreement between the decryptions by two independently reconstructed volumes. We also study how these measures can be used to define data sufficiency and its relation to spatial resolution, and the practical consequences of focusing XFEL pulses to smaller foci. This conceptual framework overcomes critical ambiguities in using Fourier Shell Correlation (FSC) as a validation measure for SPI. Finally, we show how this encryption-decryption framework naturally leads to an information-theoretic reformulation of the resolving power of XFEL-SPI, which we hope will lead to principled frameworks for experiment and instrument design.

Entities:  

Year:  2021        PMID: 33441629      PMCID: PMC7806625          DOI: 10.1038/s41598-020-79589-0

Source DB:  PubMed          Journal:  Sci Rep        ISSN: 2045-2322            Impact factor:   4.379


  33 in total

1.  Common arc method for diffraction pattern orientation.

Authors:  Gábor Bortel; Miklós Tegze
Journal:  Acta Crystallogr A       Date:  2011-10-13       Impact factor: 2.290

2.  Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight.

Authors:  N D Loh; C Y Hampton; A V Martin; D Starodub; R G Sierra; A Barty; A Aquila; J Schulz; L Lomb; J Steinbrener; R L Shoeman; S Kassemeyer; C Bostedt; J Bozek; S W Epp; B Erk; R Hartmann; D Rolles; A Rudenko; B Rudek; L Foucar; N Kimmel; G Weidenspointner; G Hauser; P Holl; E Pedersoli; M Liang; M S Hunter; M M Hunter; L Gumprecht; N Coppola; C Wunderer; H Graafsma; F R N C Maia; T Ekeberg; M Hantke; H Fleckenstein; H Hirsemann; K Nass; T A White; H J Tobias; G R Farquar; W H Benner; S P Hau-Riege; C Reich; A Hartmann; H Soltau; S Marchesini; S Bajt; M Barthelmess; P Bucksbaum; K O Hodgson; L Strüder; J Ullrich; M Frank; I Schlichting; H N Chapman; M J Bogan
Journal:  Nature       Date:  2012-06-27       Impact factor: 49.962

3.  Fourier shell correlation threshold criteria.

Authors:  Marin van Heel; Michael Schatz
Journal:  J Struct Biol       Date:  2005-09       Impact factor: 2.867

4.  Selection and orientation of different particles in single particle imaging.

Authors:  Miklós Tegze; Gábor Bortel
Journal:  J Struct Biol       Date:  2013-07-31       Impact factor: 2.867

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

Authors:  Chun Hong Yoon; 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
Journal:  Opt Express       Date:  2011-08-15       Impact factor: 3.894

6.  Imaging single cells in a beam of live cyanobacteria with an X-ray laser.

Authors:  Gijs van der Schot; Martin Svenda; Filipe R N C Maia; Max Hantke; Daniel P DePonte; M Marvin Seibert; Andrew Aquila; Joachim Schulz; Richard Kirian; Mengning Liang; Francesco Stellato; Bianca Iwan; Jakob Andreasson; Nicusor Timneanu; Daniel Westphal; F Nunes Almeida; Dusko Odic; Dirk Hasse; Gunilla H Carlsson; Daniel S D Larsson; Anton Barty; Andrew V Martin; Sebastian Schorb; Christoph Bostedt; John D Bozek; Daniel Rolles; Artem Rudenko; Sascha Epp; Lutz Foucar; Benedikt Rudek; Robert Hartmann; Nils Kimmel; Peter Holl; Lars Englert; Ne-Te Duane Loh; Henry N Chapman; Inger Andersson; Janos Hajdu; Tomas Ekeberg
Journal:  Nat Commun       Date:  2015-02-11       Impact factor: 14.919

7.  Three-dimensional reconstruction of the giant mimivirus particle with an x-ray free-electron laser.

Authors:  Tomas Ekeberg; Martin Svenda; Chantal Abergel; Filipe R N C Maia; Virginie Seltzer; Jean-Michel Claverie; Max Hantke; Olof Jönsson; Carl Nettelblad; Gijs van der Schot; Mengning Liang; Daniel P DePonte; Anton Barty; M Marvin Seibert; Bianca Iwan; Inger Andersson; N Duane Loh; Andrew V Martin; Henry Chapman; Christoph Bostedt; John D Bozek; Ken R Ferguson; Jacek Krzywinski; Sascha W Epp; Daniel Rolles; Artem Rudenko; Robert Hartmann; Nils Kimmel; Janos Hajdu
Journal:  Phys Rev Lett       Date:  2015-03-02       Impact factor: 9.161

8.  Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution.

Authors:  Miki Nakano; Osamu Miyashita; Slavica Jonic; Atsushi Tokuhisa; Florence Tama
Journal:  J Synchrotron Radiat       Date:  2018-05-30       Impact factor: 2.616

Review 9.  X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules.

Authors:  Henry N Chapman
Journal:  Annu Rev Biochem       Date:  2019-01-02       Impact factor: 23.643

10.  Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses.

Authors:  Rui Xu; Huaidong Jiang; Changyong Song; Jose A Rodriguez; Zhifeng Huang; Chien-Chun Chen; Daewoong Nam; Jaehyun Park; Marcus Gallagher-Jones; Sangsoo Kim; Sunam Kim; Akihiro Suzuki; Yuki Takayama; Tomotaka Oroguchi; Yukio Takahashi; Jiadong Fan; Yunfei Zou; Takaki Hatsui; Yuichi Inubushi; Takashi Kameshima; Koji Yonekura; Kensuke Tono; Tadashi Togashi; Takahiro Sato; Masaki Yamamoto; Masayoshi Nakasako; Makina Yabashi; Tetsuya Ishikawa; Jianwei Miao
Journal:  Nat Commun       Date:  2014-06-05       Impact factor: 14.919

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  1 in total

1.  High-quality restoration image encryption using DCT frequency-domain compression coding and chaos.

Authors:  Heping Wen; Linchao Ma; Linhao Liu; Yiming Huang; Zefeng Chen; Rui Li; Zhen Liu; Wenxing Lin; Jiahao Wu; Yunqi Li; Chongfu Zhang
Journal:  Sci Rep       Date:  2022-10-03       Impact factor: 4.996

  1 in total

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