Ptychography at the Linac Coherent Light Source in a parasitic geometry

Pound, Benjamin A.; Mertes, K. M.; Carr, Adra; Seaberg, Matthew; Hunter, Mark S.; Ward, William C.; Hunter, James F.; Sweeney, Christine; Sewell, Christopher; Weisse-Bernstein, Nina R.; Baldwin, Jon K.; Sandberg, Richard L.

doi:10.1107/s1600576720010778

Cited by 5 publications

(2 citation statements)

References 38 publications

(40 reference statements)

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“…Coherent diffraction imaging (CDI) is a lensless technique that can produce nanometer-scale resolution images by avoiding lens-imposed limitations of the traditional microscopy 1 – 7 . Ptychography 8 is a scanning CDI technique that has gained popularity because of the increasing brilliance and coherence of the synchrotron light sources 9 .…”

Section: Introductionmentioning

confidence: 99%

Scalable and accurate multi-GPU-based image reconstruction of large-scale ptychography data

Никитин

Ching

et al. 2022

Sci Rep

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While the advances in synchrotron light sources, together with the development of focusing optics and detectors, allow nanoscale ptychographic imaging of materials and biological specimens, the corresponding experiments can yield terabyte-scale volumes of data that can impose a heavy burden on the computing platform. Although graphics processing units (GPUs) provide high performance for such large-scale ptychography datasets, a single GPU is typically insufficient for analysis and reconstruction. Several works have considered leveraging multiple GPUs to accelerate the ptychographic reconstruction. However, most of these works utilize only the Message Passing Interface to handle the communications between GPUs. This approach poses inefficiency for a hardware configuration that has multiple GPUs in a single node, especially while reconstructing a single large projection, since it provides no optimizations to handle the heterogeneous GPU interconnections containing both low-speed (e.g., PCIe) and high-speed links (e.g., NVLink). In this paper, we provide an optimized intranode multi-GPU implementation that can efficiently solve large-scale ptychographic reconstruction problems. We focus on the maximum likelihood reconstruction problem using a conjugate gradient (CG) method for the solution and propose a novel hybrid parallelization model to address the performance bottlenecks in the CG solver. Accordingly, we have developed a tool, called PtyGer (Ptychographic GPU(multiple)-based reconstruction), implementing our hybrid parallelization model design. A comprehensive evaluation verifies that PtyGer can fully preserve the original algorithm’s accuracy while achieving outstanding intranode GPU scalability.

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Section: Introductionmentioning

confidence: 99%

Scalable and accurate multi-GPU-based image reconstruction of large-scale ptychography data

Никитин

Ching

et al. 2022

Sci Rep

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“…Ptychography, an imaging technique that is actively developed at synchrotron radiation facilities, has been used successfully for "at wavelength" metrology [28][29][30]. Its potential has also been demonstrated for wavefront characterisation at XFELs [31][32][33].…”

Section: Introductionmentioning

confidence: 99%

Ptychographic wavefront characterization for single-particle imaging at x-ray lasers

Daurer

Sala

Hantke

et al. 2021

Optica

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A well-characterised wavefront is important for many X-ray free-electron laser (XFEL) experiments, especially for single-particle imaging (SPI), where individual bio-molecules randomly sample a nanometerregion of highly-focused femtosecond pulses. We demonstrate high-resolution multiple-plane wavefront imaging of an ensemble of XFEL pulses, focused by Kirkpatrick-Baez (KB) mirrors, based on mixed-state ptychography, an approach letting us infer and reduce experimental sources of instability. From the recovered wavefront profiles, we show that while local photon fluence correction is crucial and possible for SPI, a small diversity of phase-tilts likely has no impact. Our detailed characterisation will aid interpretation of data from past and future SPI experiments, and provides a basis for further improvements to experimental design and reconstruction algorithms.

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

2021

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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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Ptychography at the Linac Coherent Light Source in a parasitic geometry

Cited by 5 publications

References 38 publications

Scalable and accurate multi-GPU-based image reconstruction of large-scale ptychography data

Scalable and accurate multi-GPU-based image reconstruction of large-scale ptychography data

Ptychographic wavefront characterization for single-particle imaging at x-ray lasers

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

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