SPRING: an effective and reliable framework for image reconstruction in single-particle Coherent Diffraction Imaging
Alessandro Colombo, Mario Sauppe, Andre Al Haddad, Kartik Ayyer, Morsal Babayan, Rebecca Boll, Ritika Dagar, Simon Dold, Thomas Fennel, Linos Hecht, Gregor Knop… 展开作者
Alessandro Colombo, Mario Sauppe, Andre Al Haddad, Kartik Ayyer, Morsal Babayan, Rebecca Boll, Ritika Dagar, Simon Dold, Thomas Fennel, Linos Hecht, Gregor Knopp, Katharina Kolatzki, Bruno Langbehn, Filipe R. N. C. Maia, Abhishek Mall, Parichita Mazumder, Tommaso Mazza, Yevheniy Ovcharenko, Ihsan Caner Polat, Dirk Raiser, Julian C. Schäfer-Zimmermann, Kirsten Schnorr, Marie Louise Schubert, Arezu Sehati, Jonas A. Sellberg, Björn Senfftleben, Zhou Shen, Zhibin Sun, Pamela H. W. Svensson, Paul Tümmler, Sergey Usenko, Carl Frederic Ussling, Onni Veteläinen, Simon Wächter, Noelle Walsh, Alex V. Weitnauer, Tong You, Maha Zuod, Michael Meyer, Christoph Bostedt, Davide E. Galli, Minna Patanen, Daniela Rupp
备注：
30 pages, 13 figures. Authors list updated and text revised
Coherent Diffraction Imaging (CDI) is an experimental technique to gain images of isolated structures by recording the light scattered off the sample. In principle, the sample density can be recovered from the scattered light field through a straightforward Fourier Transform operation. However, only the amplitude of the field is recorded, while the phase is lost during the measurement process and has to be retrieved by means of suitable, well-established phase retrieval algorithms. In this work, we present SPRING, an analysis framework tailored to X-ray Free Electron Laser (XFEL) single-shot single-particle diffraction data that implements the Memetic Phase Retrieval method to mitigate the shortcomings of conventional algorithms. We benchmark the approach on experimental data acquired in two experimental campaigns at SwissFEL and European XFEL. Imaging results on isolated nanostructures reveal unprecedented stability and resilience of the algorithm's behavior on the input parameters, as well as the capability of identifying the solution in conditions hardly treatable so far with conventional methods. A user-friendly implementation of SPRING is released as open-source software, aiming at being a reference tool for the coherent diffraction imaging community at XFEL and synchrotron facilities.
We present a novel adaptive machine-learning based approach for reconstructing three-dimensional (3D) crystals from coherent diffraction imaging (CDI). We represent the crystals using spherical harmonics (SH) and generate corresponding synthetic diffraction patterns. We utilize 3D convolutional neural networks (CNN) to learn a mapping between 3D diffraction volumes and the SH which describe the boundary of the physical volumes from which they were generated. We use the 3D CNN-predicted SH coefficients as the initial guesses which are then fine tuned using adaptive model independent feedback fo…
The evolution from 3rd to 4th generation synchrotron radiation (SR) sources significantly enhanced their coherence, making coherent scattering techniques such as coherent X-ray diffraction imaging (CXDI) and X-ray photon correlation spectroscopy (XPCS) more accessible. We take advantage of a coherent modes decomposition and propagation model to carry out coherence analysis and simulations of CXDI experiments for the coherent Hard X-ray Coherent Scattering (HXCS) beamline at High Energy Photon Source.
Resolution enhancement by extrapolation of coherent diffraction images: A quantitative study on the limits and a numerical study of non-binary and phase objects
We propose and experimentally demonstrate temporally low-coherent optical diffraction tomography (ODT) based on angle-scanning Mach-Zehnder interferometry. Using a digital micromirror device based on diffractive tilting, we successfully maintain full-field interference of incoherent light during every scan sequence. The ODT reconstruction principles for temporally incoherent illuminations are thoroughly reviewed and developed. Several limitations of incoherent illumination are also discussed, such as the nondispersive assumption, optical sectioning capacity, and illumination angle limitation. …
Unveiling Nano-scale Crystal Deformation using Coherent X-ray Dynamical Diffraction
Shanghai Advanced Research Institute, Chinese Academy of Sciences（上海高等研究院，中国科学院）；Condensed Matter Physics and Materials Science Division, Brookhaven National Laboratory（布鲁克海文国家实验室凝聚态物理与材料科学部）；Department of Physics, University of Science and Technology of China（中国科学技术大学物理学院）；Computational Science Initiative, Brookhaven National Laboratory（布鲁克海文国家实验室计算科学倡议）；Advanced Photon Source, Argonne National Laboratory（阿贡国家实验室先进光子源）；London Centre for Nanotechnology, University College London（伦敦纳米技术中心，伦敦大学学院）
We demonstrate that the resolution of three-dimensional (3D) real-space images obtained from Bragg x-ray coherent diffraction measurements is direction dependent. We propose and demonstrate the effectiveness of a metric to determine the spatial resolution of images that accounts for the direc- tional dependence. The measured direction dependent resolution of ~ 4-9nm is about 2 times higher than the best previously obtained 3D measurements. Finally, we quantify the relationship between the resolution of recovered real-space images and dosage, and discuss its implications in the light of next ge…
Coherent X-ray beams with energies $\geq 50$ keV can potentially enable three-dimensional imaging of atomic lattice distortion fields within individual crystallites in bulk polycrystalline materials through Bragg coherent diffraction imaging (BCDI). However, the undersampling of the diffraction signal due to Fourier space compression at high X-ray energies renders conventional phase retrieval algorithms unsuitable for three-dimensional reconstruction. To address this problem we utilize a phase retrieval method with a Fourier constraint specifically tailored for undersampled diffraction data me…
We generalize the notion of the Franhoufer diffraction from a single slit and a circular aperture to the case of partially temporal coherent and quasimonochromatic light. The problem is studied analytically and the effect of coherence length on the diffraction pattern is investigated. In this case the far-field distribution of the irradiance depends on the newly introduced parameter(decoherence parameter) which governs the deviation of the diffraction pattern from the usual one. The corrections due to temporal decoherency on the irradiance distribution in the far field is obtained. Numerical s…
Dynamical diffraction effects in single crystals produce highly monochromatic parallel X-ray beams with a mutual separation of a few micrometer and a time-delay of a few fs -the so-called echoes. This ultrafast diffraction effect is used at X-ray Free Electron Lasers in self-seeding schemes to improve beam monochromaticity. Here, we present a coherent X-ray imaging measurement of echoes from Si crystals and demonstrate that a small surface strain can be used to tune their temporal delay. These results represent a first step towards the ambitious goal of strain-tailoring new X-ray optics.
Coherent Diffraction Imaging (CDI), a technique where an object is reconstructed from a single (2D or 3D) diffraction pattern, recovers the lost diffraction phases without a priori knowledge of the extent (support) of the object, which prevents an unambiguous metric evaluation of solutions. We propose to use a 'free' log-likelihood indicator, where a small percentage of points are masked from the reconstruction algorithms, as an unbiased metric to evaluate the validity of proposed solutions, independent of the sample studied. We also show how a set of solutions can be analysed through an eigen…
Optical diffraction tomography is an indispensable tool for studying objects in three-dimensions due to its ability to accurately reconstruct scattering objects. Until now this technique has been limited to coherent light because spatial phase information is required to solve the inverse scattering problem. We introduce a method that extends optical diffraction tomography to imaging spatially incoherent contrast mechanisms such as fluorescent emission. Our strategy mimics the coherent scattering process with two spatially coherent illumination beams. The interferometric illumination pattern en…
Coherent diffraction imaging (CDI) allows the retrieval of the structure of an isolated object, such as a macromolecule, from its diffraction pattern. CDI requires the fulfilment of two conditions: the imaging radiation must be coherent and the object must be isolated. We discuss that it is possible to directly retrieve the molecular structure from its diffraction pattern which was acquired neither with coherent radiation nor from an individual molecule, provided the molecule exhibits periodicity in one direction, as in the case of fiber diffraction. We demonstrate that by applying iterative p…
Stanford University（斯坦福大学）；SLAC National Accelerator Laboratory（SLAC国家加速器实验室）
A new reference design is introduced for holographic coherent diffraction imaging. This consists in two references - "block" and "pinhole" shaped regions - placed adjacent to the imaging specimen. An efficient recovery algorithm is provided for the resulting holographic phase retrieval problem, which is based on solving a structured, overdetermined linear system. Analysis of the expected recovery error on noisy data, which is contaminated by Poisson shot noise, shows that this simple modification synergizes the individual references and hence leads to uniformly superior performance over single…
Recent advances in the field of attosecond science hold the promise of tracking electronic processes at the shortest space and time scales. Imaging methods that combine attosecond temporal with nanometer spatial resolution are currently out of reach. Coherent diffractive imaging is based on the diffraction by a sample of a quasi-monochromatic illumination with a coherence time that exceeds the duration of an attosecond pulse. Due to the extremely broad nature of attosecond spectra, novel imaging techniques are required. Here, we present an approach that enables coherent diffractive imaging wit…
The history of computing started with analog computers consisting of physical devices performing specialized functions such as predicting the trajectory of cannon balls. In modern times, this idea has been extended, for example, to ultrafast nonlinear optics serving as a surrogate analog computer to probe the behavior of complex phenomena such as rogue waves. Here we discuss a new paradigm where physical phenomena coded as an algorithm perform computational imaging tasks. Specifically, diffraction followed by coherent detection, not in its analog realization but when coded as an algorithm, bec…
We present a deep neural network to reduce coherent noise in three-dimensional quantitative phase imaging. Inspired by the cycle generative adversarial network, the denoising network was trained to learn a transform between two image domains: clean and noisy refractive index tomograms. The unique feature of this network, distinct from previous machine learning approaches employed in the optical imaging problem, is that it uses unpaired images. The learned network quantitatively demonstrated its performance and generalization capability through denoising experiments of various samples. We concl…
We propose a method to generate isolated relativistic terahertz (THz) pulses using a high-power laser irradiating a mirco-plasma-waveguide (MPW). When the laser pulse enters the MPW, high-charge electron bunches are produced and accelerated to ~ 100 MeV by the transverse magnetic modes. A substantial part of the electron energy is transferred to THz emission through coherent diffraction radiation as the electron bunches exit the MPW. We demonstrate this process with three-dimensional particle-in-cell simulations. The frequency of the radiation is determined by the incident laser duration, and …
Laser-induced transient opacity in helium nanodroplets probed by single-shot coherent diffraction
ETH Zurich（苏黎世联邦理工学院）；University of Rostock（罗斯托克大学）；Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy（马克斯·玻恩非线性光学和超快光谱研究所）；Technical University of Berlin（柏林工业大学）
Complex-field imaging is indispensable for numerous applications at wavelengths from X-ray to THz, with amplitude describing transmittance (or reflectivity) and phase revealing intrinsic structure of the target object. Coherent diffraction imaging (CDI) employs iterative phase retrieval algorithms to process diffraction measurements and is the predominant non-interferometric method to image complex fields. However, the working spectrum of CDI is quite narrow, because the diffraction measurements on which it relies require dense array detection with ultra-high dynamic range. Here we report a si…
We demonstrate a three-dimensional (3D) optical diffraction tomographic technique with optimal frequency combination (OFC-ODT) for the 3D quantitative phase imaging of unlabeled specimens. Three sets of through-focus intensity images are captured under an annular aperture and two circular apertures with different coherence parameters. The 3D phase optical transfer functions (POTF) corresponding to different illumination apertures are combined to obtain an optimally synthesized frequency response, achieving high-quality, low-noise 3D reconstructions with imaging resolution up to the incoherent …
Lensless imaging is a popular research field for the advantages of small size, wide field-of-view and low aberration in recent years. However, some traditional lensless imaging methods suffer from slow convergence, mechanical errors and conjugate solution interference, which limit its further application and development. In this work, we proposed a lensless imaging method based on spatial light modulator (SLM) with unknown modulation curve. In our imaging system, we use SLM to modulate the wavefront of object, and introduce the ptychographic scanning algorithm that is able to recover the compl…
Coherent diffractive imaging is a technique that recovers the sample image by numerically inverting its diffraction pattern. We propose a generalization of this method for the inversion of multi-wavelength data. Using this approach, we show that separate reconstructions for each wavelength can be recovered from a single polychromatic diffraction pattern. Limitations on the number of wavelengths is provided by adapting the constraint ratio to the polychromatic situation. The method's performance is demonstrated as a function of the source spectrum, the degree of complexity within the exit wave …
