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arXiv · 2303.18043

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

Sarlota Birnsteinova·Danilo E. Ferreira de Lima·Egor Sobolev·Henry J. Kirkwood·Valerio Bellucci·Richard J. Bean·Chan Kim·Jayanath C. P. Koliyadu·Tokushi Sato·Fabio Dall'Antonia·Eleni Myrto Asimakopoulou·Zisheng Yao·Khachiwan Buakor·Yuhe Zhang·Alke Meents·Henry N. Chapman·Adrian P. Mancuso·Pablo Villanueva-Perez·Patrik Vagovic
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Abstract

The X-ray microscopy technique at the European X-ray free-electron laser (EuXFEL), operating at a MHz repetition rate, provides superior contrast and spatial-temporal resolution compared to typical microscopy techniques at other X-ray sources. In both online 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 XFEL sources hinders the use of existing flat-flied normalization methods during MHz X-ray microscopy experiments. Here, we present an online dynamic flat-field correction method based on principal component analysis of dynamically evolving flat-field images. The method is used for the normalization of individual X-ray projections and has been implemented as an online analysis tool at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of EuXFEL.

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Sarlota Birnsteinova, Danilo E. Ferreira de Lima, Egor Sobolev, Henry J. Kirkwood, Valerio Bellucci, Richard J. Bean, Chan Kim, Jayanath C. P. Koliyadu, Tokushi Sato, Fabio Dall'Antonia, Eleni Myrto Asimakopoulou, Zisheng Yao, Khachiwan Buakor, Yuhe Zhang, Alke Meents, Henry N. Chapman, Adrian P. Mancuso, Pablo Villanueva-Perez, Patrik Vagovic. 2023-03-31. Online dynamic flat-field correction for MHz Microscopy data at European XFEL. https://arxiv.org/abs/2303.18043

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