Effect of radiation damage and illumination variability on signal-to-noise ratio in X-ray free-electron laser single-particle imaging

2020 ◽  
Vol 76 (6) ◽  
pp. 664-676
Author(s):  
Timur E. Gureyev ◽  
Alexander Kozlov ◽  
Andrew J. Morgan ◽  
Andrew V. Martin ◽  
Harry M. Quiney

The deterioration of both the signal-to-noise ratio and the spatial resolution in the electron-density distribution reconstructed from diffraction intensities collected at different orientations of a sample is analysed theoretically with respect to the radiation damage to the sample and the variations in the X-ray intensities illuminating different copies of the sample. The simple analytical expressions and numerical estimates obtained for models of radiation damage and incident X-ray pulses may be helpful in planning X-ray free-electron laser (XFEL) imaging experiments and in analysis of experimental data. This approach to the analysis of partially coherent X-ray imaging configurations can potentially be used for analysis of other forms of imaging where the temporal behaviour of the sample and the incident intensity during exposure may affect the inverse problem of sample reconstruction.

Crystals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1109
Author(s):  
Yue Cao ◽  
Dina Sheyfer ◽  
Zhang Jiang ◽  
Siddharth Maddali ◽  
Hoydoo You ◽  
...  

How materials evolve at thermal equilibrium and under external excitations at small length and time scales is crucial to the understanding and control of material properties. X-ray photon correlation spectroscopy (XPCS) at X-ray free electron laser (XFEL) facilities can in principle capture dynamics of materials that are substantially faster than a millisecond. However, the analysis and interpretation of XPCS data is hindered by the strongly fluctuating X-ray intensity from XFELs. Here we examine the impact of pulse-to-pulse intensity fluctuations on sequential XPCS analysis. We show that the conventional XPCS analysis can still faithfully capture the characteristic time scales, but with substantial decrease in the signal-to-noise ratio of the g2 function and increase in the uncertainties of the extracted time constants. We also demonstrate protocols for improving the signal-to-noise ratio and reducing the uncertainties.


Author(s):  
Veit Elser

Recent experiments at free-electron laser X-ray sources have been able to resolve the intensity distributions about Bragg peaks in nanocrystals of large biomolecules. Information derived from small shifts in the peak positions augment the Bragg samples of the particle intensity with samples of its gradients. Working on the assumption that the nanocrystal is entirely generated by lattice translations of a particle, an algorithm is developed that reconstructs the particle from intensities and intensity gradients. Unlike traditional direct phasing methods that require very high resolution data in order to exploit sparsity of the electron density, this method imposes no constraints on the contrast other than positivity and works well at low resolution. Successful reconstructions are demonstrated with simulatedP1 lysozyme nanocrystal data down to a signal-to-noise ratio of 2 in the intensity gradients.


2022 ◽  
Vol 93 (1) ◽  
pp. 015006
Author(s):  
Xiaolong Zhao ◽  
Ming Ye ◽  
Zhi Cao ◽  
Danyang Huang ◽  
Tingting Fan ◽  
...  

2011 ◽  
Vol 110 (10) ◽  
pp. 109902 ◽  
Author(s):  
Michael Chabior ◽  
Tilman Donath ◽  
Christian David ◽  
Manfred Schuster ◽  
Christian Schroer ◽  
...  

2004 ◽  
Vol 78 (6) ◽  
pp. 915-919 ◽  
Author(s):  
N. Kalivas ◽  
L. Costaridou ◽  
I. Kandarakis ◽  
D. Cavouras ◽  
C.D. Nomicos ◽  
...  

Author(s):  
Timur Gureyev ◽  
David M. Paganin ◽  
Alex Kozlov ◽  
Harry Quiney

2005 ◽  
Vol 77 (20) ◽  
pp. 6563-6570 ◽  
Author(s):  
Zeng Ping Chen ◽  
Julian Morris ◽  
Elaine Martin ◽  
Robert B. Hammond ◽  
Xiaojun Lai ◽  
...  

2016 ◽  
Vol 22 (3) ◽  
pp. 536-543 ◽  
Author(s):  
Jong Seok Jeong ◽  
K. Andre Mkhoyan

AbstractAcquiring an atomic-resolution compositional map of crystalline specimens has become routine practice, thus opening possibilities for extracting subatomic information from such maps. A key challenge for achieving subatomic precision is the improvement of signal-to-noise ratio (SNR) of compositional maps. Here, we report a simple and reliable solution for achieving high-SNR energy-dispersive X-ray (EDX) spectroscopy spectrum images for individual atomic columns. The method is based on standard cross-correlation aided by averaging of single-column EDX maps with modifications in the reference image. It produces EDX maps with minimal specimen drift, beam drift, and scan distortions. Step-by-step procedures to determine a self-consistent reference map with a discussion on the reliability, stability, and limitations of the method are presented here.


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