Phase retrieval for Bragg coherent diffraction imaging at high x-ray energies

Coherent diffraction imaging (CDI) is high-resolution lensless microscopy that has been applied to image a wide range of specimens using synchrotron radiation, X-ray free-electron lasers, high harmonic generation, soft X-ray lasers and electrons. Despite recent rapid advances, it remains a challenge to reconstruct fine features in weakly scattering objects such as biological specimens from noisy data. Here an effective iterative algorithm, termed oversampling smoothness (OSS), for phase retrieval of noisy diffraction intensities is presented. OSS exploits the correlation information among the pixels or voxels in the region outside of a support in real space. By properly applying spatial frequency filters to the pixels or voxels outside the support at different stages of the iterative process (i.e.a smoothness constraint), OSS finds a balance between the hybrid input–output (HIO) and error reduction (ER) algorithms to search for a global minimum in solution space, while reducing the oscillations in the reconstruction. Both numerical simulations with Poisson noise and experimental data from a biological cell indicate that OSS consistently outperforms the HIO, ER–HIO and noise robust (NR)–HIO algorithms at all noise levels in terms of accuracy and consistency of the reconstructions. It is expected that OSS will find application in the rapidly growing CDI field, as well as other disciplines where phase retrieval from noisy Fourier magnitudes is needed. TheMATLAB(The MathWorks Inc., Natick, MA, USA) source code of the OSS algorithm is freely available from http://www.physics.ucla.edu/research/imaging.

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Complex wavefront sensing based on coherent diffraction imaging using vortex modulation

Scientific Reports ◽

10.1038/s41598-021-88523-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Rujia Li ◽

Liangcai Cao

Keyword(s):

Phase Retrieval ◽

Dynamic Range ◽

A Priori ◽

Measured Intensity ◽

Physical Constraints ◽

Coherent Diffraction Imaging ◽

Effective Dynamic ◽

Ill Posed ◽

Retrieval Problem ◽

Diffraction Imaging

AbstractPhase retrieval seeks to reconstruct the phase from the measured intensity, which is an ill-posed problem. A phase retrieval problem can be solved with physical constraints by modulating the investigated complex wavefront. Orbital angular momentum has been recently employed as a type of reliable modulation. The topological charge l is robust during propagation when there is atmospheric turbulence. In this work, topological modulation is used to solve the phase retrieval problem. Topological modulation offers an effective dynamic range of intensity constraints for reconstruction. The maximum intensity value of the spectrum is reduced by a factor of 173 under topological modulation when l is 50. The phase is iteratively reconstructed without a priori knowledge. The stagnation problem during the iteration can be avoided using multiple topological modulations.

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A high-pressure cryocooling method for protein crystals and biological samples with reduced background X-ray scatter

Journal of Applied Crystallography ◽

10.1107/s0021889812045013 ◽

2012 ◽

Vol 46 (1) ◽

pp. 234-241 ◽

Cited By ~ 11

Author(s):

Chae Un Kim ◽

Jennifer L. Wierman ◽

Richard Gillilan ◽

Enju Lima ◽

Sol M. Gruner

Keyword(s):

High Pressure ◽

Biological Samples ◽

Protein Crystal ◽

High Background ◽

X Ray ◽

Coherent Diffraction Imaging ◽

X Ray Scattering ◽

Alternative Method ◽

Helium Gas ◽

Diffraction Imaging

High-pressure cryocooling has been developed as an alternative method for cryopreservation of macromolecular crystals and successfully applied for various technical and scientific studies. The method requires the preservation of crystal hydration as the crystal is pressurized with dry helium gas. Previously, crystal hydration was maintained either by coating crystals with a mineral oil or by enclosing crystals in a capillary which was filled with crystallization mother liquor. These methods are not well suited to weakly diffracting crystals because of the relatively high background scattering from the hydrating materials. Here, an alternative method of crystal hydration, called capillary shielding, is described. The specimen is kept hydratedviavapor diffusion in a shielding capillary while it is being pressure cryocooled. After cryocooling, the shielding capillary is removed to reduce background X-ray scattering. It is shown that, compared to previous crystal-hydration methods, the new hydration method produces superior crystal diffraction with little sign of crystal damage. Using the new method, a weakly diffracting protein crystal may be properly pressure cryocooled with little or no addition of external cryoprotectants, and significantly reduced background scattering can be observed from the resulting sample. Beyond the applications for macromolecular crystallography, it is shown that the method has great potential for the preparation of noncrystalline hydrated biological samples for coherent diffraction imaging with future X-ray sources.

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Phase retrieval with data-driven dual alternating direction method of multipliers for coherent diffraction imaging

10.1364/ntm.2021.ntu1c.2 ◽

2021 ◽

Author(s):

Li Song ◽

Edmund Y. Lam

Keyword(s):

Phase Retrieval ◽

Alternating Direction Method ◽

Data Driven ◽

Method Of Multipliers ◽

Coherent Diffraction Imaging ◽

Alternating Direction ◽

Diffraction Imaging

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Simulation of Coherent Diffraction Imaging Based on Scanning Transimission X-Ray Microscopy of Shanghai Synchrotron Radiation Facility

Acta Optica Sinica ◽

10.3788/aos201131.0418001 ◽

2011 ◽

Vol 31 (4) ◽

pp. 0418001

Author(s):

谭兴兴 Tan Xingxing ◽

刘海岗 Liu Haigang ◽

郭智 Guo Zhi ◽

吴衍青 Wu Yanqing ◽

许子健 Xu Zijian ◽

...

Keyword(s):

Synchrotron Radiation ◽

Shanghai Synchrotron Radiation Facility ◽

X Ray ◽

Coherent Diffraction Imaging ◽

Diffraction Imaging

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Multi-beam X-ray ptychography for high-throughput coherent diffraction imaging

Scientific Reports ◽

10.1038/s41598-020-76412-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Yudong Yao ◽

Yi Jiang ◽

Jeffrey A. Klug ◽

Michael Wojcik ◽

Evan R. Maxey ◽

...

Keyword(s):

Fresnel Zone ◽

Field Of View ◽

X Ray ◽

Single Beam ◽

Coherent Diffraction Imaging ◽

Diffraction Imaging ◽

Extended Field ◽

Resolution Imaging ◽

Diffraction Patterns ◽

Scanning Mechanism

Abstract X-ray ptychography is a rapidly developing coherent diffraction imaging technique that provides nanoscale resolution on extended field-of-view. However, the requirement of coherence and the scanning mechanism limit the throughput of ptychographic imaging. In this paper, we propose X-ray ptychography using multiple illuminations instead of single illumination in conventional ptychography. Multiple locations of the sample are simultaneously imaged by spatially separated X-ray beams, therefore, the obtained field-of-view in one scan can be enlarged by a factor equal to the number of illuminations. We have demonstrated this technique experimentally using two X-ray beams focused by a house-made Fresnel zone plate array. Two areas of the object and corresponding double illuminations were successfully reconstructed from diffraction patterns acquired in one scan, with image quality similar with those obtained by conventional single-beam ptychography in sequence. Multi-beam ptychography approach increases the imaging speed, providing an efficient way for high-resolution imaging of large extended specimens.

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Continuous scanning for Bragg coherent X-ray imaging

Scientific Reports ◽

10.1038/s41598-020-69678-5 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Ni Li ◽

Maxime Dupraz ◽

Longfei Wu ◽

Steven J. Leake ◽

Andrea Resta ◽

...

Keyword(s):

Flow Reactor ◽

Light Sources ◽

Pt Nanoparticle ◽

Strain Fields ◽

X Ray ◽

Coherent Diffraction Imaging ◽

Scan Time ◽

X Ray Imaging ◽

Continuous Scanning ◽

Diffraction Imaging

Abstract We explore the use of continuous scanning during data acquisition for Bragg coherent diffraction imaging, i.e., where the sample is in continuous motion. The fidelity of continuous scanning Bragg coherent diffraction imaging is demonstrated on a single Pt nanoparticle in a flow reactor at $$400\,^\circ \hbox {C}$$ 400 ∘ C in an Ar-based gas flowed at 50 ml/min. We show a reduction of 30% in total scan time compared to conventional step-by-step scanning. The reconstructed Bragg electron density, phase, displacement and strain fields are in excellent agreement with the results obtained from conventional step-by-step scanning. Continuous scanning will allow to minimise sample instability under the beam and will become increasingly important at diffraction-limited storage ring light sources.

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