Pulse-to-pulse wavefront sensing at free-electron lasers using ptychography

Sala, Simone; Daurer, Benedikt J.; Odstrčil, Michal; Capotondi, Flavio; Pedersoli, Emanuele; Hantke, Max F.; Manfredda, Michele; Loh, N. Duane; Thibault, Pierre; Maia, Filipe R. N. C.

doi:10.1107/s1600576720006913

Cited by 17 publications

(13 citation statements)

References 44 publications

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“…Equation 12expresses the undamaged electron density in the sample via the coherent modes that can be retrieved from experimental data, collected in the presence of radiation damage, using phase retrieval algorithms (Whitehead et al, 2009;Quiney, 2010;Sala et al, 2019) and the eigenvectors of the matrix SP obtained from the theoretical model. Importantly, the first summation in equation 12can always be truncated at a finite k = M, which corresponds to the singularvalue decomposition (SVD) of the matrix SP, SPx = P k k hx; v k i u k (Golub & Van Loan, 1989).…”

Section: Modal Decompositionmentioning

confidence: 99%

“…These modes can in principle be retrieved from the 3D diffraction fluence, collected in the presence of radiation damage, and a priori information about the sample (Quiney, 2010;Quiney & Nugent, 2011;Curwood et al, 2013). A different algorithm for solving a generalized phase retrieval problem (Thibault & Menzel, 2013) has been successfully used to retrieve ten coherent modes from the diffraction data collected in an XFEL imaging experiment (Sala et al, 2019).…”

Section: Modal Decompositionmentioning

confidence: 99%

“…An application of phase retrieval algorithms which assume full coherence and retrieve the phase of a single mode will therefore yield such a damaged electron density. Generalized phase retrieval algorithms capable of retrieving multiple coherent modes have been reported in the literature (Whitehead et al, 2009;Quiney, 2010;Sala et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Recovery of undamaged electron-density maps in the presence of damage-induced partial coherence in single-particle imaging

Kozlov

Gureyev

Paganin

et al. 2020

Int Union Crystallogr J

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Resolving the electronic structure of single biological molecules in their native state was among the primary motivations behind X-ray free-electron lasers. The ultra-short pulses they produce can outrun the atomic motion induced by radiation damage, but the electronic structure of the sample is still significantly modified from its original state. This paper explores the decoherence of the scattered signal induced by temporal evolution of the electronic structure in the sample molecule. It is shown that the undamaged electron density of a single-molecule sample can often be retrieved using only the two most occupied modes from the coherent mode decomposition of the partially coherent diffraction fluence.

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Section: Modal Decompositionmentioning

confidence: 99%

Section: Modal Decompositionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Recovery of undamaged electron-density maps in the presence of damage-induced partial coherence in single-particle imaging

Kozlov

Gureyev

Paganin

et al. 2020

Int Union Crystallogr J

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“…This constrains the transfer of some of the most powerful imaging methods developed for synchrotron radiation to XFELs, namely ptychography (Rodenburg et al, 2007) on the nano scale; or correspondingly on meso-and macroscopic scales interferometric (Weitkamp et al, 2005), and analyzer-based imaging methods (Chapman et al, 1997). Ptychography with XFEL radiation has been demonstrated for static specimens (Schropp et al, 2013;Sala et al, 2020), and can be parallelized to some extent (Hirose et al, 2020), but not yet with single-pulse capability. Coherent diffraction imaging (CDI) (Miao et al, 1999), on the other hand, has been successfully implemented for single-pulse XFEL applications, including small biological particles such as bacteria or viruses (Seibert et al, 2011;Neutze et al, 2000;Sobolev et al, 2019;Bogan et al, 2008;Robinson et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Single-pulse phase-contrast imaging at free-electron lasers in the hard X-ray regime

Hagemann¹,

Vassholz²,

Hoeppe³

et al. 2021

J Synchrotron Radiat

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X-ray free-electron lasers (XFELs) have opened up unprecedented opportunities for time-resolved nano-scale imaging with X-rays. Near-field propagation-based imaging, and in particular near-field holography (NFH) in its high-resolution implementation in cone-beam geometry, can offer full-field views of a specimen's dynamics captured by single XFEL pulses. To exploit this capability, for example in optical-pump/X-ray-probe imaging schemes, the stochastic nature of the self-amplified spontaneous emission pulses, i.e. the dynamics of the beam itself, presents a major challenge. In this work, a concept is presented to address the fluctuating illumination wavefronts by sampling the configuration space of SASE pulses before an actual recording, followed by a principal component analysis. This scheme is implemented at the MID (Materials Imaging and Dynamics) instrument of the European XFEL and time-resolved NFH is performed using aberration-corrected nano-focusing compound refractive lenses. Specifically, the dynamics of a micro-fluidic water-jet, which is commonly used as sample delivery system at XFELs, is imaged. The jet exhibits rich dynamics of droplet formation in the break-up regime. Moreover, pump–probe imaging is demonstrated using an infrared pulsed laser to induce cavitation and explosion of the jet.

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“…De Caro et al (2020) use it to image some peculiarly shaped nanocrystals in a polymer matrix. Sala et al (2020) show us how ptychography can be used with a range of sources and a variety of purposes by imaging the wavefront of an X-ray free-electron laser.…”

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confidence: 99%

Introduction to the special issue on Ptychography: software and technical developments

2021

Self Cite

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Ptychography is an X-ray technique that achieves resolutions of one billionth of a metre, can reach a macroscopic field of view, and has the capability to retrieve chemical or magnetic contrast, among other features. It includes variants such as ptycho-tomography and spectro-ptychography, which are some of the most computationally intensive techniques being developed at X-ray light sources around the world.In the past few years ptychography has grown into a diverse landscape of methods to address ever more complex systems. These techniques involve beautiful mathematics, from harmonic analysis and algebraic geometry to complex numerical analysis.The Ptycho Developers 2019 workshop held at Berkeley Laboratory on 3-5 June 2019 was attended by 60 participants from five continents. The goal of the workshop was to bring together developers and practitioners of ptychography to assess the current landscape of available algorithms and software, investigate commonalities, and discuss a range of topics, from required theoretical and algorithmic advancements and unmet needs to practical issues of implementation and deployment. Other topics included workflows, beamlines, optics and high-performance computing solutions.Several ideas presented at the Berkeley workshop were later turned into manuscripts. These manuscripts formed the seed that grew into this virtual special issue, being complemented by diverse contributions from around the world.This special issue provides us with an opportunity to take a glimpse of some of the developments addressed in the workshop. The 14 articles it contains cover a broad variety of subjects but can be roughly divided into the following groups:(1) A new speckle-based ptychography variant is introduced by Morgan, Murray, Prasciolu et al. (2020), aimed at wavefront metrology. This is accompanied by two further manuscripts, headed by the same author: one of them (Morgan, Murray, Quiney et al., 2020) describing speckle-tracking, an open-source software package for the analysis of data from the newly developed X-ray speckle-tracking ptychography variant, and the other (Morgan, Quiney et al., 2020) showcasing its first application, aiding the fabrication of wedged multi-layer Laue lenses by providing a way to accurately characterize them.(2) Du et al. (2020) address the dose requirements of multiple X-ray microscopy techniques with detailed numerical simulations and conclude that it is the photon fluence, and not the experimental geometry, that limits the resolution of a properly conducted measurement.(3) Two manuscripts highlight a broad range of direct applications of ptychography. De Caro et al. (2020) use it to image some peculiarly shaped nanocrystals in a polymer matrix. Sala et al. (2020) show us how ptychography can be used with a range of sources and a variety of purposes by imaging the wavefront of an X-ray free-electron laser.(4) Significant advances in instrumentation are presented by three manuscripts. Khant et al. (2020) show us that NanoMAX is ready for ptycho-tomographic measuremen...

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Pulse-to-pulse wavefront sensing at free-electron lasers using ptychography

Cited by 17 publications

References 44 publications

Recovery of undamaged electron-density maps in the presence of damage-induced partial coherence in single-particle imaging

Recovery of undamaged electron-density maps in the presence of damage-induced partial coherence in single-particle imaging

Single-pulse phase-contrast imaging at free-electron lasers in the hard X-ray regime

Introduction to the special issue on Ptychography: software and technical developments

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