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Online dynamic flat-field correction for MHz microscopy data at European XFEL

Birnsteinova, Sarlota ; Ferreira de Lima, Danilo E ; Sobolev, Egor ; Kirkwood, Henry J ; Bellucci, Valerio ; Bean, Richard J ; Kim, Chan ; Koliyadu, Jayanath C P ; Sato, Tokushi and Dall'Antonia, Fabio , et al. (2023) In Journal of Synchrotron Radiation 30(6). p.1030-1037
Abstract

The high pulse intensity and repetition rate of the European X-ray Free-Electron Laser (EuXFEL) provide superior temporal resolution compared with other X-ray sources. In combination with MHz X-ray microscopy techniques, it offers a unique opportunity to achieve superior contrast and spatial resolution in applications demanding high temporal resolution. In both live visualization and offline data analysis for microscopy experiments, baseline normalization is essential for further processing steps such as phase retrieval and modal decomposition. In addition, access to normalized projections during data acquisition can play an important role in decision-making and improve the quality of the data. However, the stochastic nature of X-ray... (More)

The high pulse intensity and repetition rate of the European X-ray Free-Electron Laser (EuXFEL) provide superior temporal resolution compared with other X-ray sources. In combination with MHz X-ray microscopy techniques, it offers a unique opportunity to achieve superior contrast and spatial resolution in applications demanding high temporal resolution. In both live visualization and offline data analysis for microscopy experiments, baseline normalization is essential for further processing steps such as phase retrieval and modal decomposition. In addition, access to normalized projections during data acquisition can play an important role in decision-making and improve the quality of the data. However, the stochastic nature of X-ray free-electron laser sources hinders the use of standard flat-field normalization methods during MHz X-ray microscopy experiments. Here, an online (i.e. near real-time) dynamic flat-field correction method based on principal component analysis of dynamically evolving flat-field images is presented. The method is used for the normalization of individual X-ray projections and has been implemented as a near real-time analysis tool at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of EuXFEL.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Synchrotron Radiation
volume
30
issue
6
pages
1030 - 1037
publisher
International Union of Crystallography
external identifiers
  • scopus:85176495382
  • pmid:37729072
ISSN
1600-5775
DOI
10.1107/S1600577523007336
language
English
LU publication?
yes
additional info
open access.
id
5ba880de-81f6-4d38-968a-a22a766d2b43
date added to LUP
2023-09-28 08:35:18
date last changed
2024-04-19 11:34:45
@article{5ba880de-81f6-4d38-968a-a22a766d2b43,
  abstract     = {{<p>The high pulse intensity and repetition rate of the European X-ray Free-Electron Laser (EuXFEL) provide superior temporal resolution compared with other X-ray sources. In combination with MHz X-ray microscopy techniques, it offers a unique opportunity to achieve superior contrast and spatial resolution in applications demanding high temporal resolution. In both live visualization and offline data analysis for microscopy experiments, baseline normalization is essential for further processing steps such as phase retrieval and modal decomposition. In addition, access to normalized projections during data acquisition can play an important role in decision-making and improve the quality of the data. However, the stochastic nature of X-ray free-electron laser sources hinders the use of standard flat-field normalization methods during MHz X-ray microscopy experiments. Here, an online (i.e. near real-time) dynamic flat-field correction method based on principal component analysis of dynamically evolving flat-field images is presented. The method is used for the normalization of individual X-ray projections and has been implemented as a near real-time analysis tool at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of EuXFEL.</p>}},
  author       = {{Birnsteinova, Sarlota and Ferreira de Lima, Danilo E and Sobolev, Egor and Kirkwood, Henry J and Bellucci, Valerio and Bean, Richard J and Kim, Chan and Koliyadu, Jayanath C P and Sato, Tokushi and Dall'Antonia, Fabio and Asimakopoulou, Eleni Myrto and Yao, Zisheng and Buakor, Khachiwan and Zhang, Yuhe and Meents, Alke and Chapman, Henry N and Mancuso, Adrian P and Villanueva-Perez, Pablo and Vagovič, Patrik}},
  issn         = {{1600-5775}},
  language     = {{eng}},
  month        = {{11}},
  number       = {{6}},
  pages        = {{1030--1037}},
  publisher    = {{International Union of Crystallography}},
  series       = {{Journal of Synchrotron Radiation}},
  title        = {{Online dynamic flat-field correction for MHz microscopy data at European XFEL}},
  url          = {{http://dx.doi.org/10.1107/S1600577523007336}},
  doi          = {{10.1107/S1600577523007336}},
  volume       = {{30}},
  year         = {{2023}},
}