Stefano Marchesini

SLAC National Accelerator Laboratory

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Henry N. Chapman

Universität Hamburg

Anton Barty

Deutsches Elektronen-Synchrotron DESY

David A. Shapiro

Lawrence Berkeley National Laboratory

S. Bajt

Max Planck Institute for the Structure and Dynamics of Matter

Filipe R. N. C. Maia

Lawrence Berkeley National Laboratory

Stefan P. Hau‐Riege

Lawrence Livermore National Laboratory

Uwe Weierstall

Arizona State University

Michael J. Bogan

SLAC National Accelerator Laboratory

Matthias Frank

Lawrence Livermore National Laboratory

János Hajdu

Extreme Light Infrastructure Beamlines

Cooperative Institutions

Lawrence Berkeley National Laboratory

203

SLAC National Accelerator Laboratory

181

Stanford University

University of California, Berkeley

Deutsches Elektronen-Synchrotron DESY

Universität Hamburg

Lawrence Livermore National Laboratory

Menlo School

Linac Coherent Light Source

Center for Free-Electron Laser Science

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Augmented projections for ptychographic imaging

Inverse Problems (2013)

Stefano Marchesini André Schirotzek Chao Yang Hau‐Tieng Wu Filipe R. N. C. Maia

Ptychography is a popular technique to achieve diffraction limited resolution images of a two or three dimensional sample using high frame rate detectors.We introduce a relaxation of common projection algorithms to account for instabilities given by intensity and background fluctuations, position errors, or poor calibration using multiplexing illumination.This relaxation introduces an additional phasing optimization at every step that enhances the convergence rate of common projection algorithms.Numerical tests exhibit the exact recovery of the object and the perturbations when there is high redundancy in the data.

Ptychography

Position (finance)

10.1088/0266-5611/29/11/115009

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Citations (52)

Aerosol Imaging with a Soft X-Ray Free Electron Laser

Aerosol Science and Technology (2010)

Michael J. Bogan Sébastien Boutet Henry N. Chapman Stefano Marchesini Anton Barty

Lasers have long played a critical role in the advancement of aerosol science. A new regime of ultrafast laser technology has recently be realized, the world's first soft x-ray free electron laser. The Free electron LASer in Hamburg, FLASH, user facility produces a steady source of 10 femtosecond pulses of 7–32 nm x-rays with 1012 photons per pulse. The high brightness, short wavelength, and high repetition rate (> 500 pulses per second) of this laser offers unique capabilities for aerosol characterization. Here we use FLASH to perform the highest resolution imaging of single PM2.5 aerosol particles in flight to date. We resolve to 35 nm the morphology of fibrous and aggregated spherical carbonaceous nanoparticles that existed for less than two milliseconds in vacuum. Our result opens the possibility for high spatial- and time-resolved single particle aerosol dynamics studies, filling a critical technological need in aerosol science.

Particle (ecology)

Free-electron laser

10.1080/02786820903485800

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Citations (47)

High-resolution ab initio three-dimensional x-ray diffraction microscopy

Journal of the Optical Society of America A (2006)

Henry N. Chapman Anton Barty Stefano Marchesini Aleksandr Noy Stefan P. Hau‐Riege

Coherent x-ray diffraction microscopy is a method of imaging nonperiodic isolated objects at resolutions limited, in principle, by only the wavelength and largest scattering angles recorded. We demonstrate x-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the three-dimensional diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a nonperiodic object. We also construct two-dimensional images of thick objects with greatly increased depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution with x-ray undulator radiation and establishes the techniques to be used in atomic-resolution ultrafast imaging at x-ray free-electron laser sources. © 2006 Optical Society of America OCIS codes: 340.7460, 110.1650, 110.6880, 100.5070, 100.6890, 070.2590, 180.6900.

Coherent diffraction imaging

Undulator

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Ring artifact reduction via multiscale nonlocal collaborative filtering of spatially correlated noise

Journal of Synchrotron Radiation (2021)

Ymir Mäkinen Stefano Marchesini Alessandro Foi

X-ray micro-tomography systems often suffer severe ring artifacts in reconstructed images. These artifacts are caused by defects in the detector, calibration errors, and fluctuations producing streak noise in the raw sinogram data. In this work, these streaks are modeled in the sinogram domain as additive stationary correlated noise upon logarithmic transformation. Based on this model, a streak removal procedure is proposed where the Block-Matching and 3-D (BM3D) filtering algorithm is applied across multiple scales, achieving state-of-the-art performance in both real and simulated data. Specifically, the proposed fully automatic procedure allows for attenuation of streak noise and the corresponding ring artifacts without creating major distortions common to other streak removal algorithms.

Streak

Artifact (error)

10.1107/s1600577521001910

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Citations (7)

Data preparation and evaluation techniques for x-ray diffraction microscopy

Optics Express (2010)

Jan Steinbrener Johanna Nelson Weker Xiaojing Huang Stefano Marchesini David A. Shapiro

The post-experiment processing of X-ray Diffraction Microscopy data is often time-consuming and difficult. This is mostly due to the fact that even if a preliminary result has been reconstructed, there is no definitive answer as to whether or not a better result with more consistently retrieved phases can still be obtained. We show here that the first step in data analysis, the assembly of two-dimensional diffraction patterns from a large set of raw diffraction data, is crucial to obtaining reconstructions of highest possible consistency. We have developed software that automates this process and results in consistently accurate diffraction patterns. We have furthermore derived some criteria of validity for a tool commonly used to assess the consistency of reconstructions, the phase retrieval transfer function, and suggest a modified version that has improved utility for judging reconstruction quality.

Data set

10.1364/oe.18.018598

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Citations (40)

Mesoscale morphology of airborne core–shell nanoparticle clusters: x-ray laser coherent diffraction imaging

Journal of Physics B Atomic Molecular and Optical Physics (2013)

Emanuele Pedersoli N. Duane Loh Flavio Capotondi Christina Y. Hampton Raymond G. Sierra

Unraveling the complex morphology of functional materials like core–shell nanoparticles and its evolution in different environments is still a challenge. Only recently has the single-particle coherent diffraction imaging (CDI), enabled by the ultrabright femtosecond free-electron laser pulses, provided breakthroughs in understanding mesoscopic morphology of nanoparticulate matter. Here, we report the first CDI results for Co@SiO2 core–shell nanoparticles randomly clustered in large airborne aggregates, obtained using the x-ray free-electron laser at the Linac Coherent Light Source. Our experimental results compare favourably with simulated diffraction patterns for clustered Co@SiO2 nanoparticles with ∼10 nm core diameter and ∼30 nm shell outer diameter, which confirms the ability to resolve the mesoscale morphology of complex metastable structures. The findings in this first morphological study of core–shell nanomaterials are a solid base for future time-resolved studies of dynamic phenomena in complex nanoparticulate matter using x-ray lasers.

Morphology

10.1088/0953-4075/46/16/164033

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Citations (14)

SHARP: a distributed GPU-based ptychographic solver

Journal of Applied Crystallography (2016)

Stefano Marchesini Harinarayan Krishnan Benedikt J. Daurer David A. Shapiro Talita Perciano

Ever brighter light sources, fast parallel detectors and advances in phase retrieval methods have made ptychography a practical and popular imaging technique. Compared to previous techniques, ptychography provides superior robustness and resolution at the expense of more advanced and time-consuming data analysis. By taking advantage of massively parallel architectures, high-throughput processing can expedite this analysis and provide microscopists with immediate feedback. These advances allow real-time imaging at wavelength-limited resolution, coupled with a large field of view. This article describes a set of algorithmic and computational methodologies used at the Advanced Light Source and US Department of Energy light sources. These are packaged as a CUDA-based software environment named SHARP (http://camera.lbl.gov/sharp), aimed at providing state-of-the-art high-throughput ptychography reconstructions for the coming era of diffraction-limited light sources.

Ptychography

Robustness

10.1107/s1600576716008074

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Citations (89)

Soft x-ray ptychography studies of nanoscale magnetic and structural correlations in thin SmCo5 films

Applied Physics Letters (2016)

Xiaowen Shi Peter Fischer V. Neu D. Elefant J. C. T. Lee

High spatial resolution magnetic x-ray spectromicroscopy at x-ray photon energies near the cobalt L3 resonance was applied to probe an amorphous 50 nm thin SmCo5 film prepared by off-axis pulsed laser deposition onto an x-ray transparent 200 nm thin Si3N4 membrane. Alternating gradient magnetometry shows a strong in-plane anisotropy and an only weak perpendicular magnetic anisotropy, which is confirmed by magnetic transmission soft x-ray microscopy images showing over a field of view of 10 μm a primarily stripe-like domain pattern but with local labyrinth-like domains. Soft x-ray ptychography in amplitude and phase contrast was used to identify and characterize local magnetic and structural features over a field of view of 1 μm with a spatial resolution of about 10 nm. There, the magnetic labyrinth domain patterns are accompanied by nanoscale structural inclusions that are primarily located in close proximity to the magnetic domain walls. Our analysis suggests that these inclusions are nanocrystalline Sm2Co17 phases with nominally in-plane magnetic anisotropy.

Nanocrystalline material

Film plane

10.1063/1.4942776

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Citations (86)

Data analytics at the Linac Coherent Light Source

Acta Crystallographica Section A Foundations and Advances (2023)

J. P. Thayer Richard O. Claus D. S. Damiani M. M. Dubrovin C. J. B. Ford

10.1107/s2053273323090290

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Phase retrieval and saddle-point optimization

Journal of the Optical Society of America A (2007)

Stefano Marchesini

Iterative algorithms with feedback are among the most powerful and versatile optimization methods for phase retrieval. Among these, the hybrid input-output algorithm has demonstrated practical solutions to giga-element nonlinear phase retrieval problems, escaping local minima and producing images at resolutions beyond the capabilities of lens-based optical methods. Here the input-output iteration is improved by a lower-dimensional subspace saddle-point optimization.

Maxima and minima

Saddle point

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