1
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Lin D, Jiang Y, Deng J, Marin FS, Di ZW. Efficient boundary-guided scanning for high-resolution X-ray ptychography. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:129-135. [PMID: 38084593 PMCID: PMC10833418 DOI: 10.1107/s1600577523009657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/06/2023] [Indexed: 01/09/2024]
Abstract
In the realm of X-ray ptychography experiments, a considerable amount of ptychography scans are typically performed within a field of view encompassing the target sample. While it is crucial to obtain overlapping scans in small increments over the region of interest for achieving high-resolution sample reconstruction, a significant number of these scans often redundantly measure the empty background within the wide field of view. To address this inefficiency, an innovative algorithm is proposed that introduces automatic guidance for data acquisition. The algorithm first directs the scan point to actively search for the object of interest within the field of view. Subsequently, it intelligently scans along the perimeter of the sample, strategically acquiring measurements exclusively within the boundary of the region of interest. By employing this approach, a reduction in the number of measurements required to obtain high-resolution reconstruction images is demonstrated, as compared with conventional raster scanning methods. Furthermore, the automatic guidance provided by the algorithm offers the added advantage of saving valuable time during the reconstruction process. Through practical implementation on real experiments, these findings showcase the efficacy of the proposed algorithm in enhancing the efficiency and accuracy of X-ray ptychography experiments. This novel approach holds immense potential for advancing sample analysis and imaging techniques in various scientific disciplines.
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Affiliation(s)
- Dergan Lin
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Yi Jiang
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Junjing Deng
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Fabricio S. Marin
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Zichao Wendy Di
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
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2
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Abe M, Ishiguro N, Uematsu H, Takazawa S, Kaneko F, Takahashi Y. X-ray ptychographic and fluorescence microscopy using virtual single-pixel imaging based deconvolution with accurate probe images. OPTICS EXPRESS 2023; 31:26027-26039. [PMID: 37710473 DOI: 10.1364/oe.495733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/15/2023] [Indexed: 09/16/2023]
Abstract
Simultaneous measurement of X-ray ptychography and fluorescence microscopy allows high-resolution and high-sensitivity observations of the microstructure and trace-element distribution of a sample. In this paper, we propose a method for improving scanning fluorescence X-ray microscopy (SFXM) images, in which the SFXM image is deconvolved via virtual single-pixel imaging using different probe images for each scanning point obtained by X-ray ptychographic reconstruction. Numerical simulations confirmed that this method can increase the spatial resolution while suppressing artifacts caused by probe imprecision, e.g., probe position errors and wavefront changes. The method also worked well in synchrotron radiation experiments to increase the spatial resolution and was applied to the observation of S element maps of ZnS particles.
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3
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Quinn PD, Cacho-Nerin F, Gomez-Gonzalez MA, Parker JE, Poon T, Walker JM. Differential phase contrast for quantitative imaging and spectro-microscopy at a nanoprobe beamline. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:200-207. [PMID: 36601938 PMCID: PMC9814065 DOI: 10.1107/s1600577522010633] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 11/04/2022] [Indexed: 06/13/2023]
Abstract
The interaction of a focused X-ray beam with a sample in a scanning probe experiment can provide a variety of information about the interaction volume. In many scanning probe experiments X-ray fluorescence (XRF) is supplemented with measurements of the transmitted or scattered intensity using a pixelated detector. The automated extraction of different signals from an area pixelated detector is described, in particular the methodology for extracting differential phase contrast (DPC) is demonstrated and different processing methods are compared across a range of samples. The phase shift of the transmitted X-ray beam by the sample, extracted from DPC, is also compared with ptychography measurements to provide a qualitative and quantitative comparison. While ptychography produces a superior image, DPC can offer a simple, flexible method for phase contrast imaging which can provide fast results and feedback during an experiment; furthermore, for many science problems, such as registration of XRF in a lighter matrix, DPC can provide sufficient information to meet the experimental aims. As the DPC technique is a quantitative measurement, it can be expanded to spectroscopic studies and a demonstration of DPC for spectro-microscopy measurements is presented. Where ptychography can separate the absorption and phase shifts by the sample, quantitative interpretation of a DPC image or spectro-microscopy signal can only be performed directly when absorption is negligible or where the absorption contribution is known and the contributions can be fitted.
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Affiliation(s)
- Paul D. Quinn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Fernando Cacho-Nerin
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Miguel A. Gomez-Gonzalez
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Julia E. Parker
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Timothy Poon
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Jessica M. Walker
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
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4
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Deng J, Yao Y, Jiang Y, Chen S, Mooney TM, Klug JA, Marin FS, Roehrig C, Yue K, Preissner C, Cai Z, Lai B, Vogt S. High-resolution ptychographic imaging enabled by high-speed multi-pass scanning. OPTICS EXPRESS 2022; 30:26027-26042. [PMID: 36236801 DOI: 10.1364/oe.460232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/18/2022] [Indexed: 06/16/2023]
Abstract
As a coherent diffraction imaging technique, ptychography provides high-spatial resolution beyond Rayleigh's criterion of the focusing optics, but it is also sensitively affected by the decoherence coming from the spatial and temporal variations in the experiment. Here we show that high-speed ptychographic data acquisition with short exposure can effectively reduce the impact from experimental variations. To reach a cumulative dose required for a given resolution, we further demonstrate that a continuous multi-pass scan via high-speed ptychography can achieve high-resolution imaging. This low-dose scan strategy is shown to be more dose-efficient, and has potential for radiation-sensitive sample studies and time-resolved imaging.
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5
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Yu X, Nikitin V, Ching DJ, Aslan S, Gürsoy D, Biçer T. Scalable and accurate multi-GPU-based image reconstruction of large-scale ptychography data. Sci Rep 2022; 12:5334. [PMID: 35351971 PMCID: PMC8964803 DOI: 10.1038/s41598-022-09430-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 11/01/2021] [Indexed: 11/10/2022] Open
Abstract
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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Affiliation(s)
- Xiaodong Yu
- Data Science and Learning Division, Argonne National Laboratory, 9700 Cass Avenue, Lemont, IL, 60439, USA.
| | - Viktor Nikitin
- X-ray Science Division, Argonne National Laboratory, 9700 Cass Avenue, Lemont, IL, 60439, USA
| | - Daniel J Ching
- X-ray Science Division, Argonne National Laboratory, 9700 Cass Avenue, Lemont, IL, 60439, USA
| | - Selin Aslan
- X-ray Science Division, Argonne National Laboratory, 9700 Cass Avenue, Lemont, IL, 60439, USA
| | - Doğa Gürsoy
- X-ray Science Division, Argonne National Laboratory, 9700 Cass Avenue, Lemont, IL, 60439, USA.,Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Tekin Biçer
- Data Science and Learning Division, Argonne National Laboratory, 9700 Cass Avenue, Lemont, IL, 60439, USA. .,X-ray Science Division, Argonne National Laboratory, 9700 Cass Avenue, Lemont, IL, 60439, USA.
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6
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Jones MWM, van Riessen GA, Phillips NW, Schrank CE, Hinsley GN, Afshar N, Reinhardt J, de Jonge MD, Kewish CM. High-speed free-run ptychography at the Australian Synchrotron. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:480-487. [PMID: 35254312 PMCID: PMC8900864 DOI: 10.1107/s1600577521012856] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Over the last decade ptychography has progressed rapidly from a specialist ultramicroscopy technique into a mature method accessible to non-expert users. However, to improve scientific value ptychography data must reconstruct reliably, with high image quality and at no cost to other correlative methods. Presented here is the implementation of high-speed ptychography used at the Australian Synchrotron on the XFM beamline, which includes a free-run data collection mode where dead time is eliminated and the scan time is optimized. It is shown that free-run data collection is viable for fast and high-quality ptychography by demonstrating extremely high data rate acquisition covering areas up to 352 000 µm2 at up to 140 µm2 s-1, with 13× spatial resolution enhancement compared with the beam size. With these improvements, ptychography at velocities up to 250 µm s-1 is approaching speeds compatible with fast-scanning X-ray fluorescence microscopy. The combination of these methods provides morphological context for elemental and chemical information, enabling unique scientific outcomes.
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Affiliation(s)
- Michael W. M. Jones
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Grant A. van Riessen
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
- Melbourne Centre for Nanofabrication, Clayton, Victoria 3168, Australia
| | - Nicholas W. Phillips
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | - Christoph E. Schrank
- School of Earth and Atmospheric Sciences, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Gerard N. Hinsley
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Nader Afshar
- Australian Nuclear Science and Technology Organisation, Australian Synchrotron, Clayton, Victoria 3168, Australia
| | - Juliane Reinhardt
- Australian Nuclear Science and Technology Organisation, Australian Synchrotron, Clayton, Victoria 3168, Australia
| | - Martin D. de Jonge
- Australian Nuclear Science and Technology Organisation, Australian Synchrotron, Clayton, Victoria 3168, Australia
| | - Cameron M. Kewish
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
- Australian Nuclear Science and Technology Organisation, Australian Synchrotron, Clayton, Victoria 3168, Australia
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7
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Cipiccia S, Brun F, Di Trapani V, Rau C, Batey DJ. Dual energy X-ray beam ptycho-fluorescence imaging. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1916-1920. [PMID: 34738946 PMCID: PMC8570202 DOI: 10.1107/s1600577521008675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
X-ray ptychography and X-ray fluorescence are complementary nanoscale imaging techniques, providing structural and elemental information, respectively. Both methods acquire data by scanning a localized beam across the sample. X-ray ptychography processes the transmission signal of a coherent illumination interacting with the sample, to produce images with a resolution finer than the illumination spot and step size. By enlarging both the spot and the step size, the technique can cover extended regions efficiently. X-ray fluorescence records the emitted spectra as the sample is scanned through the localized beam and its spatial resolution is limited by the spot and step size. The requisites for fast ptychography and high-resolution fluorescence appear incompatible. Here, a novel scheme that mitigates the difference in requirements is proposed. The method makes use of two probes of different sizes at the sample, generated by using two different energies for the probes and chromatic focusing optics. The different probe sizes allow to reduce the number of acquisition steps for the joint fluorescence-ptychography scan compared with a standard single beam scan, while imaging the same field of view. The new method is demonstrated experimentally using two undulator harmonics, a Fresnel zone plate and an energy discriminating photon counting detector.
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Affiliation(s)
- Silvia Cipiccia
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, United Kingdom
| | - Francesco Brun
- Department of Engineering and Architecture, University of Trieste, Via Alfonso Valerio 6/1, Trieste 34127, Italy
| | - Vittorio Di Trapani
- Department of Physics, University of Trieste, Via Alfonso Valerio 6/1, Trieste 34127, Italy
| | - Christoph Rau
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, United Kingdom
| | - Darren J. Batey
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, United Kingdom
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8
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Hirose M, Shimomura K, Higashino T, Ishiguro N, Takahashi Y. Nanoscale determination of interatomic distance by ptychography-EXAFS method using advanced Kirkpatrick-Baez mirror focusing optics. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:455-461. [PMID: 32153284 DOI: 10.1107/s1600577519017004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
This work demonstrates a combination technique of X-ray ptychography and the extended X-ray absorption fine structure (ptychography-EXAFS) method, which can determine the interatomic distances of bulk materials at the nanoscale. In the high-resolution ptychography-EXAFS method, it is necessary to use high-intense coherent X-rays with a uniform wavefront in a wide energy range, hence a ptychographic measurement system installed with advanced Kirkpatrick-Baez mirror focusing optics is developed and its performance is evaluated. Ptychographic diffraction patterns of micrometre-size MnO particles are collected by using this system at 139 energies between 6.504 keV and 7.114 keV including the Mn K absorption edge, and then the EXAFS of MnO is derived from the reconstructed images. By analyzing the EXAFS spectra obtained from a 48 nm × 48 nm region, the nanoscale bond lengths of the first and second coordination shells of MnO are determined. The present approach has great potential to elucidate the unclarified relationship among the morphology, electronic state and atomic arrangement of inhomogeneous bulk materials with high spatial resolution.
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Affiliation(s)
- Makoto Hirose
- Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0855, Japan
| | - Kei Shimomura
- Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0855, Japan
| | - Takaya Higashino
- Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0855, Japan
| | - Nozomu Ishiguro
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo, Hyogo 679-5148, Japan
| | - Yukio Takahashi
- Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0855, Japan
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9
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Multimodal X-ray imaging of nanocontainer-treated macrophages and calcium distribution in the perilacunar bone matrix. Sci Rep 2020; 10:1784. [PMID: 32019946 PMCID: PMC7000813 DOI: 10.1038/s41598-020-58318-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/23/2019] [Indexed: 11/16/2022] Open
Abstract
Studies of biological systems typically require the application of several complementary methods able to yield statistically-relevant results at a unique level of sensitivity. Combined X-ray fluorescence and ptychography offer excellent elemental and structural imaging contrasts at the nanoscale. They enable a robust correlation of elemental distributions with respect to the cellular morphology. Here we extend the applicability of the two modalities to higher X-ray excitation energies, permitting iron mapping. Using a long-range scanning setup, we applied the method to two vital biomedical cases. We quantified the iron distributions in a population of macrophages treated with Mycobacterium-tuberculosis-targeting iron-oxide nanocontainers. Our work allowed to visualize the internalization of the nanocontainer agglomerates in the cytosol. From the iron areal mass maps, we obtained a distribution of antibiotic load per agglomerate and an average areal concentration of nanocontainers in the agglomerates. In the second application we mapped the calcium content in a human bone matrix in close proximity to osteocyte lacunae (perilacunar matrix). A concurrently acquired ptychographic image was used to remove the mass-thickness effect from the raw calcium map. The resulting ptychography-enhanced calcium distribution allowed then to observe a locally lower degree of mineralization of the perilacunar matrix.
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10
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Abstract
For the past several decades, synchrotron radiation has been extensively used to measure the spatial distribution and chemical affinity of elements found in trace concentrations (<few μg/g) in animal and human tissues. Intense and highly focused (lateral size of several micrometers) X-ray beams combined with small steps of photon energy tuning (2-3 eV) of synchrotron radiation allowed X-ray fluorescence (XRF) and X-ray absorption spectroscopy (XAS) techniques to nondestructively and simultaneously detect trace elements as well as identify their chemical affinity and speciation in situ, respectively. Although limited by measurement time and radiation damage to the tissue, these techniques are commonly used to obtain two-dimensional and three-dimensional maps of several elements at synchrotron facilities around the world. The spatial distribution and chemistry of the trace elements obtained is then correlated to the targeted anatomical structures and to the biological functions (normal or pathological). For example, synchrotron-based in vitro studies of various human tissues showed significant differences between the normal and pathological distributions of metallic trace elements such as iron, zinc, copper, and lead in relation to human diseases ranging from Parkinson's disease and cancer to osteoporosis and osteoarthritis. Current research effort is aimed at not only measuring the abnormal elemental distributions associated with various diseases, but also indicate or discover possible biological mechanisms that could explain such observations. While a number of studies confirmed and strengthened previous knowledge, others revealed or suggested new possible roles of trace elements or provided a more accurate spatial distribution in relation to the underlying histology. This area of research is at the intersection of several current fundamental and applied scientific inquiries such as metabolomics, medicine, biochemistry, toxicology, food science, health physics, and environmental and public health.
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11
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Deng J, Preissner C, Klug JA, Mashrafi S, Roehrig C, Jiang Y, Yao Y, Wojcik M, Wyman MD, Vine D, Yue K, Chen S, Mooney T, Wang M, Feng Z, Jin D, Cai Z, Lai B, Vogt S. The Velociprobe: An ultrafast hard X-ray nanoprobe for high-resolution ptychographic imaging. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:083701. [PMID: 31472643 DOI: 10.1063/1.5103173] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Motivated by the advanced photon source upgrade, a new hard X-ray microscope called "Velociprobe" has been recently designed and built for fast ptychographic imaging with high spatial resolution. We are addressing the challenges of high-resolution and fast scanning with novel hardware designs, advanced motion controls, and new data acquisition strategies, including the use of high-bandwidth interferometric measurements. The use of granite, air-bearing-supported stages provides the necessary long travel ranges for coarse motion to accommodate real samples and variable energy operation while remaining highly stable during fine scanning. Scanning the low-mass zone plate enables high-speed and high-precision motion of the probe over the sample. With an advanced control algorithm implemented in a closed-loop feedback system, the setup achieves a position resolution (3σ) of 2 nm. The instrument performance is evaluated by 2D fly-scan ptychography with our developed data acquisition strategies. A spatial resolution of 8.8 nm has been demonstrated on a Au test sample with a detector continuous frame rate of 200 Hz. Using a higher flux X-ray source provided by double-multilayer monochromator, we achieve 10 nm resolution for an integrated circuit sample in an ultrafast scan with a detector's full continuous frame rate of 3000 Hz (0.33 ms per exposure), resulting in an outstanding imaging rate of 9 × 104 resolution elements per second.
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Affiliation(s)
- Junjing Deng
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Curt Preissner
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Jeffrey A Klug
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Sheikh Mashrafi
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Christian Roehrig
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Yi Jiang
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Yudong Yao
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Michael Wojcik
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Max D Wyman
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - David Vine
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Ke Yue
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Tim Mooney
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Maoyu Wang
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon 97331, USA
| | - Zhenxing Feng
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon 97331, USA
| | - Dafei Jin
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Zhonghou Cai
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Barry Lai
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Stefan Vogt
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
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12
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Odstrčil M, Lebugle M, Guizar-Sicairos M, David C, Holler M. Towards optimized illumination for high-resolution ptychography. OPTICS EXPRESS 2019; 27:14981-14997. [PMID: 31163938 DOI: 10.1364/oe.27.014981] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We present a systematic study, where effects of the illumination probe design on ptychography reconstruction quality are evaluated under well-controlled conditions. The illumination probe was created using Fresnel zone-plate (FZP) optics with locally displaced zones to provide a fine control over perturbations of the illumination wavefront. We show that optimally designed wavefront modulations not only reduce bias and variance in the reconstruction of the lowest spatial frequencies but also lead to improved imaging resolution and reduction of artefacts compared to a conventional FZP. Both these factors are important for quantitative accuracy and resolution of ptychographic tomography. Our work furthers the understanding of the important characteristics of an optimal illumination for high-resolution X-ray ptychography and how to design optimal FZP wavefront modulations for different applications of ptychographic imaging. These findings are applicable and relevant for ptychography using optical, EUV, and X-ray photons as well as electrons.
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13
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Jones MWM, Phillips NW, Abbey B, Hare DJ, van Riessen GA, Vine DJ, de Jonge MD, McColl G. Simultaneous nanostructure and chemical imaging of intact whole nematodes. Chem Commun (Camb) 2019; 55:1052-1055. [DOI: 10.1039/c8cc09664c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Accurately locating biologically relevant elements at high resolution: simultaneous ptychography and fluorescence imaging of large specimens comes of age.
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Affiliation(s)
- Michael W. M. Jones
- Central Analytical Research Facility
- Institute of Future Environments
- Queensland University of Technology
- Brisbane
- Australia
| | - Nicholas W. Phillips
- ARC Centre of Excellence in Advanced Molecular Imaging
- La Trobe Institute for Molecular Sciences
- La Trobe University
- Victoria 3086
- Australia
| | - Brian Abbey
- Department of Engineering Science
- University of Oxford
- Oxford
- UK
- Department of Chemistry and Physics
| | - Dominic J. Hare
- The Florey Institute of Neuroscience and Mental Health
- The University of Melbourne
- Victoria
- Australia
| | - Grant A. van Riessen
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Victoria 3086
- Australia
| | - David J. Vine
- X-ray Science Division
- Advanced Photon Source
- Argonne National Laboratory
- Argonne
- USA
| | | | - Gawain McColl
- The Florey Institute of Neuroscience and Mental Health
- The University of Melbourne
- Victoria
- Australia
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14
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Deng J, Lo YH, Gallagher-Jones M, Chen S, Pryor A, Jin Q, Hong YP, Nashed YSG, Vogt S, Miao J, Jacobsen C. Correlative 3D x-ray fluorescence and ptychographic tomography of frozen-hydrated green algae. SCIENCE ADVANCES 2018; 4:eaau4548. [PMID: 30406204 PMCID: PMC6214637 DOI: 10.1126/sciadv.aau4548] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/24/2018] [Indexed: 05/20/2023]
Abstract
Accurate knowledge of elemental distributions within biological organisms is critical for understanding their cellular roles. The ability to couple this knowledge with overall cellular architecture in three dimensions (3D) deepens our understanding of cellular chemistry. Using a whole, frozen-hydrated Chlamydomonas reinhardtii cell as an example, we report the development of 3D correlative microscopy through a combination of simultaneous cryogenic x-ray ptychography and x-ray fluorescence microscopy. By taking advantage of a recently developed tomographic reconstruction algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), we produce high-quality 3D maps of the unlabeled alga's cellular ultrastructure and elemental distributions within the cell. We demonstrate GENFIRE's ability to outperform conventional tomography algorithms and to further improve the reconstruction quality by refining the experimentally intended tomographic angles. As this method continues to advance with brighter coherent light sources and more efficient data handling, we expect correlative 3D x-ray fluorescence and ptychographic tomography to be a powerful tool for probing a wide range of frozen-hydrated biological specimens, ranging from small prokaryotes such as bacteria, algae, and parasites to large eukaryotes such as mammalian cells, with applications that include understanding cellular responses to environmental stimuli and cell-to-cell interactions.
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Affiliation(s)
- Junjing Deng
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Yuan Hung Lo
- Department of Physics and Astronomy and California NanoSystems Institute, University of California Los Angeles, CA 90095, USA
- Department of Bioengineering, University of California Los Angeles, CA 90095, USA
| | - Marcus Gallagher-Jones
- Department of Physics and Astronomy and California NanoSystems Institute, University of California Los Angeles, CA 90095, USA
- Department of Chemistry & Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095-1570, USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alan Pryor
- Department of Physics and Astronomy and California NanoSystems Institute, University of California Los Angeles, CA 90095, USA
| | - Qiaoling Jin
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - Young Pyo Hong
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - Youssef S. G. Nashed
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Stefan Vogt
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Jianwei Miao
- Department of Physics and Astronomy and California NanoSystems Institute, University of California Los Angeles, CA 90095, USA
- Corresponding author. (J.M.); (C.J.)
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Corresponding author. (J.M.); (C.J.)
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15
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Ching DJ, Hidayetoğlu M, Biçer T, Gürsoy D. Rotation-as-fast-axis scanning-probe x-ray tomography: the importance of angular diversity for fly-scan modes. APPLIED OPTICS 2018; 57:8780-8789. [PMID: 30461860 DOI: 10.1364/ao.57.008780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/15/2018] [Indexed: 06/09/2023]
Abstract
We investigate the effects of angular diversity on image-reconstruction quality of scanning-probe x-ray tomography for both fly- and step-mode data collection. We propose probe-coverage maps as a tool for both visualizing and quantifying the distribution of probe interactions with the object. We show that data sampling with more angular diversity yields better tomographic image reconstruction as long as it does not come at the cost of not covering some voxels in the object. Therefore, for fly-mode data collection, rotation-as-fast-axis (RAFA) trajectories are superior to raster or other non-RAFA trajectories because they allow for the increasing of angular diversity without sacrificing spatial coverage uniformity. In contrast, for step-mode data collection and a fixed measurement budget, increasing angular diversity can come at the cost of not covering some voxels, and may not be desired. This study has implications for how scanning-probe microscopes should be collecting data in order to make the most of limited resources.
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16
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New EJ, Wimmer VC, Hare DJ. Promises and Pitfalls of Metal Imaging in Biology. Cell Chem Biol 2017; 25:7-18. [PMID: 29153850 DOI: 10.1016/j.chembiol.2017.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/02/2017] [Accepted: 10/18/2017] [Indexed: 10/18/2022]
Abstract
A picture may speak a thousand words, but if those words fail to form a coherent sentence there is little to be learned. As cutting-edge imaging technology now provides us the tools to decipher the multitude of roles played by metals and metalloids in molecular, cellular, and developmental biology, as well as health and disease, it is time to reflect on the advances made in imaging, the limitations discovered, and the future of a burgeoning field. In this Perspective, the current state of the art is discussed from a self-imposed contrarian position, as we not only highlight the major advances made over the years but use them as teachable moments to zoom in on challenges that remain to be overcome. We also describe the steps being taken toward being able to paint a completely undisturbed picture of cellular metal metabolism, which is, metaphorically speaking, the Holy Grail of the discipline.
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Affiliation(s)
- Elizabeth J New
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Verena C Wimmer
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Dominic J Hare
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia; Elemental Bio-imaging Facility, University of Technology Sydney, Broadway, NSW 2007, Australia; Department of Pathology, The University of Melbourne, Parkville, VIC 3052, Australia.
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17
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Hémonnot CYJ, Köster S. Imaging of Biological Materials and Cells by X-ray Scattering and Diffraction. ACS NANO 2017; 11:8542-8559. [PMID: 28787573 DOI: 10.1021/acsnano.7b03447] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cells and biological materials are large objects in comparison to the size of internal components such as organelles and proteins. An understanding of the functions of these nanoscale elements is key to elucidating cellular function. In this review, we describe the advances in X-ray scattering and diffraction techniques for imaging biological systems at the nanoscale. We present a number of principal technological advances in X-ray optics and development of sample environments. We identify radiation damage as one of the most severe challenges in the field, thus rendering the dose an important parameter when putting different X-ray methods in perspective. Furthermore, we describe different successful approaches, including scanning and full-field techniques, along with prominent examples. Finally, we present a few recent studies that combined several techniques in one experiment in order to collect highly complementary data for a multidimensional sample characterization.
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Affiliation(s)
- Clément Y J Hémonnot
- Institute for X-Ray Physics, University of Goettingen , Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Northwestern Argonne Institute of Science and Engineering, Northwestern University , 9700 South Cass Avenue, Argonne, Illinois 60439, United States
- Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Sarah Köster
- Institute for X-Ray Physics, University of Goettingen , Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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18
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X-ray ptychographic and fluorescence microscopy of frozen-hydrated cells using continuous scanning. Sci Rep 2017; 7:445. [PMID: 28348401 PMCID: PMC5428657 DOI: 10.1038/s41598-017-00569-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/03/2017] [Indexed: 01/19/2023] Open
Abstract
X-ray microscopy can be used to image whole, unsectioned cells in their native hydrated state. It complements the higher resolution of electron microscopy for submicrometer thick specimens, and the molecule-specific imaging capabilites of fluorescence light microscopy. We describe here the first use of fast, continuous x-ray scanning of frozen hydrated cells for simultaneous sub-20 nm resolution ptychographic transmission imaging with high contrast, and sub-100 nm resolution deconvolved x-ray fluorescence imaging of diffusible and bound ions at native concentrations, without the need to add specific labels. By working with cells that have been rapidly frozen without the use of chemical fixatives, and imaging them under cryogenic conditions, we are able to obtain images with well preserved structural and chemical composition, and sufficient stability against radiation damage to allow for multiple images to be obtained with no observable change.
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19
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Jones MWM, Phillips NW, van Riessen GA, Abbey B, Vine DJ, Nashed YSG, Mudie ST, Afshar N, Kirkham R, Chen B, Balaur E, de Jonge MD. Simultaneous X-ray fluorescence and scanning X-ray diffraction microscopy at the Australian Synchrotron XFM beamline. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:1151-1157. [PMID: 27577770 DOI: 10.1107/s1600577516011917] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 07/21/2016] [Indexed: 06/06/2023]
Abstract
Owing to its extreme sensitivity, quantitative mapping of elemental distributions via X-ray fluorescence microscopy (XFM) has become a key microanalytical technique. The recent realisation of scanning X-ray diffraction microscopy (SXDM) meanwhile provides an avenue for quantitative super-resolved ultra-structural visualization. The similarity of their experimental geometries indicates excellent prospects for simultaneous acquisition. Here, in both step- and fly-scanning modes, robust, simultaneous XFM-SXDM is demonstrated.
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Affiliation(s)
- Michael W M Jones
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Nicholas W Phillips
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Victoria 3086, Australia
| | - Grant A van Riessen
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Brian Abbey
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Victoria 3086, Australia
| | - David J Vine
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Youssef S G Nashed
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Stephen T Mudie
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Nader Afshar
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Robin Kirkham
- CSIRO Manufacturing, Clayton, Victoria 3168, Australia
| | - Bo Chen
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Victoria 3086, Australia
| | - Eugeniu Balaur
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Victoria 3086, Australia
| | - Martin D de Jonge
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
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20
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Jones MWM, Elgass KD, Junker MD, de Jonge MD, van Riessen GA. Molar concentration from sequential 2-D water-window X-ray ptychography and X-ray fluorescence in hydrated cells. Sci Rep 2016; 6:24280. [PMID: 27067957 PMCID: PMC4828672 DOI: 10.1038/srep24280] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 03/22/2016] [Indexed: 01/25/2023] Open
Abstract
Recent developments in biological X-ray microscopy have allowed structural information and elemental distribution to be simultaneously obtained by combining X-ray ptychography and X-ray fluorescence microscopy. Experimentally, these methods can be performed simultaneously; however, the optimal conditions for each measurement may not be compatible. Here, we combine two distinct measurements of ultrastructure and elemental distribution, with each measurement performed under optimised conditions. By combining optimised ptychography and fluorescence information we are able to determine molar concentrations from two-dimensional images, allowing an investigation into the interactions between the environment sensing filopodia in fibroblasts and extracellular calcium. Furthermore, the biological ptychography results we present illustrate a point of maturity where the technique can be applied to solve significant problems in structural biology.
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Affiliation(s)
- M W M Jones
- Australian Synchrotron, 800 Blackburn Rd, Clayton, 3168, Australia.,ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, 3086, Australia
| | - K D Elgass
- Monash Micro Imaging, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, 3168, Australia
| | - M D Junker
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - M D de Jonge
- Australian Synchrotron, 800 Blackburn Rd, Clayton, 3168, Australia
| | - G A van Riessen
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
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21
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De Caro L, Altamura D, Arciniegas M, Siliqi D, Kim MR, Sibillano T, Manna L, Giannini C. Ptychographic Imaging of Branched Colloidal Nanocrystals Embedded in Free-Standing Thick Polystyrene Films. Sci Rep 2016; 6:19397. [PMID: 26775682 PMCID: PMC4726119 DOI: 10.1038/srep19397] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 12/07/2015] [Indexed: 12/30/2022] Open
Abstract
Research on composite materials is facing, among others, the challenging task of incorporating nanocrystals, and their superstructures, in polymer matrices. Electron microscopy can typically image nanometre-scale structures embedded in thin polymer films, but not in films that are micron size thick. Here, X-ray Ptychography was used to visualize, with a resolution of a few tens of nanometers, how CdSe/CdS octapod-shaped nanocrystals self-assemble in polystyrene films of 24 ± 4 μm, providing a unique means for non-destructive investigation of nanoparticles distribution and organization in thick polymer films.
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Affiliation(s)
- Liberato De Caro
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, via Amendola 122/O, 70126 Bari, Italy
| | - Davide Altamura
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, via Amendola 122/O, 70126 Bari, Italy
| | - Milena Arciniegas
- Istituto Italiano di Tecnologia (IIT), via Morego 30, IT-16163 Genova, Italy
| | - Dritan Siliqi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, via Amendola 122/O, 70126 Bari, Italy
| | - Mee R Kim
- Istituto Italiano di Tecnologia (IIT), via Morego 30, IT-16163 Genova, Italy
| | - Teresa Sibillano
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, via Amendola 122/O, 70126 Bari, Italy
| | - Liberato Manna
- Istituto Italiano di Tecnologia (IIT), via Morego 30, IT-16163 Genova, Italy
| | - Cinzia Giannini
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, via Amendola 122/O, 70126 Bari, Italy
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22
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Deng J, Vine DJ, Chen S, Nashed YSG, Jin Q, Peterka T, Vogt S, Jacobsen C. Advances and challenges in cryo ptychography at the Advanced Photon Source. AIP CONFERENCE PROCEEDINGS 2016; 1696:020030. [PMID: 27293302 PMCID: PMC4898057 DOI: 10.1063/1.4937524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Ptychography has emerged as a nondestructive tool to quantitatively study extended samples at a high spatial resolution. In this manuscript, we report on recent developments from our team. We have combined cryo ptychography and fluorescence microscopy to provide simultaneous views of ultrastructure and elemental composition, we have developed multi-GPU parallel computation to speed up ptychographic reconstructions, and we have implemented fly-scan ptychography to allow for faster data acquisition. We conclude with a discussion of future challenges in high-resolution 3D ptychography.
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Affiliation(s)
- J Deng
- Applied Physics, Northwestern University, Evanston IL 60208, USA
| | - D J Vine
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - S Chen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Y S G Nashed
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Q Jin
- Department of Physics & Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - T Peterka
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - S Vogt
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - C Jacobsen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA; Department of Physics & Astronomy and Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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23
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Hong YP, Chen S, Jacobsen C. A New Workflow for x-ray fluorescence tomography: MAPSToTomoPy. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2015; 9592. [PMID: 27103755 DOI: 10.1117/12.2194162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
X-ray fluorescence tomography involves the acquisition of a series of 2D x-ray fluorescence datasets between which a specimen is rotated. At the Advanced Photon Source at Argonne National Laboratory, the workflow at beamlines 2-ID-E and 21-ID-D (the Bionanoprobe, a cryogenic microscope system) has included the use of the program MAPS for obtaining elemental concentrations from 2D images, and the program TomoPy which was developed to include several tomographic reconstruction methods for x-ray transmission data. In the past, fluorescence projection images from an individual chemical element were hand-assembled into a 3D dataset for reconstruction using interactive tools such as ImageJ. We describe here the program MAPSToTomoPy, which provides a graphical user interface (GUI) to control a workflow between MAPS and TomoPy, with tools for visualizing the sinograms of projection image sequences from particular elements and to use these to help correct misalignments of the rotation axis. The program also provides an integrated output of the 3D distribution of the detected elements for subsequent 3D visualization packages.
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Affiliation(s)
- Young Pyo Hong
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave., Argonne IL 60439-4837 USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave., Argonne IL 60439-4837 USA; Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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24
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Deng J, Vine DJ, Chen S, Nashed YSG, Peterka T, Ross R, Vogt S, Jacobsen C. Opportunities and limitations for combined fly-scan ptychography and fluorescence microscopy. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2015; 9592. [PMID: 27041790 DOI: 10.1117/12.2190749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
X-ray fluorescence offers unparalleled sensitivity for imaging the nanoscale distribution of trace elements in micrometer thick samples, while x-ray ptychography offers an approach to image light element containing structures at a resolution beyond that of the x-ray lens used. These methods can be used in combination, and in continuous scan mode for rapid data acquisition when using multiple probe mode reconstruction methods. We discuss here the opportunities and limitations of making use of additional information provided by ptychography to improve x-ray fluorescence images in two ways: by using position-error-correction algorithms to correct for scan distortions in fluorescence scans, and by considering the signal-to-noise limits on previously-demonstrated ptychographic probe deconvolution methods. This highlights the advantages of using a combined approach.
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Affiliation(s)
- Junjing Deng
- Applied Physics, Northwestern University, Evanston, IL 60208, USA
| | - David J Vine
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Si Chen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Youssef S G Nashed
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Tom Peterka
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Rob Ross
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Stefan Vogt
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Chris Jacobsen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA; Department of Physics & Astronomy, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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25
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Strain in a silicon-on-insulator nanostructure revealed by 3D x-ray Bragg ptychography. Sci Rep 2015; 5:9827. [PMID: 25984829 PMCID: PMC4434906 DOI: 10.1038/srep09827] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 03/19/2015] [Indexed: 11/24/2022] Open
Abstract
Progresses in the design of well-defined electronic band structure and dedicated
functionalities rely on the high control of complex architectural device nano-scaled
structures. This includes the challenging accurate description of strain fields in
crystalline structures, which requires non invasive and three-dimensional (3D)
imaging methods. Here, we demonstrate in details how x-ray Bragg ptychography can be
used to quantify in 3D a displacement field in a lithographically patterned
silicon-on-insulator structure. The image of the crystalline properties, which
results from the phase retrieval of a coherent intensity data set, is obtained from
a well-controlled optimized process, for which all steps are detailed. These results
confirm the promising perspectives of 3D Bragg ptychography for the investigation of
complex nano-structured crystals in material science.
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26
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Deng J, Nashed YSG, Chen S, Phillips NW, Peterka T, Ross R, Vogt S, Jacobsen C, Vine DJ. Continuous motion scan ptychography: characterization for increased speed in coherent x-ray imaging. OPTICS EXPRESS 2015; 23:5438-51. [PMID: 25836777 PMCID: PMC4394751 DOI: 10.1364/oe.23.005438] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/07/2015] [Accepted: 01/12/2015] [Indexed: 05/18/2023]
Abstract
Ptychography is a coherent diffraction imaging (CDI) method for extended objects in which diffraction patterns are acquired sequentially from overlapping coherent illumination spots. The object's complex transmission function can be reconstructed from those diffraction patterns at a spatial resolution limited only by the scattering strength of the object and the detector geometry. Most experiments to date have positioned the illumination spots on the sample using a move-settle-measure sequence in which the move and settle steps can take longer to complete than the measure step. We describe here the use of a continuous "fly-scan" mode for ptychographic data collection in which the sample is moved continuously, so that the experiment resembles one of integrating the diffraction patterns from multiple probe positions. This allows one to use multiple probe mode reconstruction methods to obtain an image of the object and also of the illumination function. We show in simulations, and in x-ray imaging experiments, some of the characteristics of fly-scan ptychography, including a factor of 25 reduction in the data acquisition time. This approach will become increasingly important as brighter x-ray sources are developed, such as diffraction limited storage rings.
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Affiliation(s)
- Junjing Deng
- Applied Physics Program, Northwestern University, Evanston, IL 60208,
USA
| | - Youssef S. G. Nashed
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439,
USA
| | - Si Chen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439,
USA
| | - Nicholas W. Phillips
- Australian Research Council, Centre of Excellence for Advanced Molecular Imaging, La Trobe University, VIC 3086,
Australia
- CSIRO Manufacturing Flagship, Parkville, Victoria 3052,
Australia
| | - Tom Peterka
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439,
USA
| | - Rob Ross
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439,
USA
| | - Stefan Vogt
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439,
USA
| | - Chris Jacobsen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439,
USA
- Department of Physics & Astronomy, Northwestern University, Evanston, IL 60208,
USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208,
USA
| | - David J. Vine
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439,
USA
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27
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Thibault P, Guizar-Sicairos M, Menzel A. Coherent imaging at the diffraction limit. Erratum. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:469. [PMID: 25723951 PMCID: PMC4344364 DOI: 10.1107/s1600577515001575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 12/24/2014] [Indexed: 06/04/2023]
Abstract
A correction to the article by Thibault et al. [J. Synchrotron Rad. (2014), 21, 1011–1018] is given.
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Affiliation(s)
- Pierre Thibault
- Department of Physics and Astronomy, University College London, UK
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28
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Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae. Proc Natl Acad Sci U S A 2015; 112:2314-9. [PMID: 25675478 DOI: 10.1073/pnas.1413003112] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolution beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and ∼90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. This combined approach offers a way to study the role of trace elements in their structural context.
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de Jonge MD, Ryan CG, Jacobsen CJ. X-ray nanoprobes and diffraction-limited storage rings: opportunities and challenges of fluorescence tomography of biological specimens. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:1031-47. [PMID: 25177992 PMCID: PMC4151681 DOI: 10.1107/s160057751401621x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 07/11/2014] [Indexed: 05/22/2023]
Abstract
X-ray nanoprobes require coherent illumination to achieve optic-limited resolution, and so will benefit directly from diffraction-limited storage rings. Here, the example of high-resolution X-ray fluorescence tomography is focused on as one of the most voracious demanders of coherent photons, since the detected signal is only a small fraction of the incident flux. Alternative schemes are considered for beam delivery, sample scanning and detectors. One must consider as well the steps before and after the X-ray experiment: sample preparation and examination conditions, and analysis complexity due to minimum dose requirements and self-absorption. By understanding the requirements and opportunities for nanoscale fluorescence tomography, one gains insight into the R&D challenges in optics and instrumentation needed to fully exploit the source advances that diffraction-limited storage rings offer.
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Affiliation(s)
- Martin D. de Jonge
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Christopher G. Ryan
- CSIRO Earth Science and Research Engineering, Clayton, Victoria 3168, Australia
| | - Chris J. Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
- Department of Physics, Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
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Guizar-Sicairos M, Johnson I, Diaz A, Holler M, Karvinen P, Stadler HC, Dinapoli R, Bunk O, Menzel A. High-throughput ptychography using Eiger: scanning X-ray nano-imaging of extended regions. OPTICS EXPRESS 2014; 22:14859-70. [PMID: 24977581 DOI: 10.1364/oe.22.014859] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The smaller pixel size and high frame rate of next-generation photon counting pixel detectors opens new opportunities for the application of X-ray coherent diffractive imaging (CDI). In this manuscript we demonstrate fast image acquisition for ptychography using an Eiger detector. We achieve above 25,000 resolution elements per second, or an effective dwell time of 40 μs per resolution element, when imaging a 500 μm × 290 μm region of an integrated electronic circuit with 41 nm resolution. We further present the application of a scheme of sharing information between image parts that allows the field of view to exceed the range of the piezoelectric scanning system and requirements on the stability of the illumination to be relaxed.
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Fu G, Meng LJ, Eng P, Newville M, Vargas P, La Riviere P. Experimental demonstration of novel imaging geometries for x-ray fluorescence computed tomography. Med Phys 2014; 40:061903. [PMID: 23718594 DOI: 10.1118/1.4801907] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PURPOSE X-ray fluorescence computed tomography (XFCT) is an emerging imaging modality that maps the three-dimensional distribution of elements, generally metals, in ex vivo specimens and potentially in living animals and humans. At present, it is generally performed at synchrotrons, taking advantage of the high flux of monochromatic x rays, but recent work has demonstrated the feasibility of using laboratory-based x-ray tube sources. In this paper, the authors report the development and experimental implementation of two novel imaging geometries for mapping of trace metals in biological samples with ∼50-500 μm spatial resolution. METHODS One of the new imaging approaches involves illuminating and scanning a single slice of the object and imaging each slice's x-ray fluorescent emissions using a position-sensitive detector and a pinhole collimator. The other involves illuminating a single line through the object and imaging the emissions using a position-sensitive detector and a slit collimator. They have implemented both of these using synchrotron radiation at the Advanced Photon Source. RESULTS The authors show that it is possible to achieve 250 eV energy resolution using an electron multiplying CCD operating in a quasiphoton-counting mode. Doing so allowed them to generate elemental images using both of the novel geometries for imaging of phantoms and, for the second geometry, an osmium-stained zebrafish. CONCLUSIONS The authors have demonstrated the feasibility of these two novel approaches to XFCT imaging. While they use synchrotron radiation in this demonstration, the geometries could readily be translated to laboratory systems based on tube sources.
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Affiliation(s)
- Geng Fu
- Department of Nuclear, Plasma, and Radiological Engineering, The University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
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Zürch M, Kern C, Spielmann C. XUV coherent diffraction imaging in reflection geometry with low numerical aperture. OPTICS EXPRESS 2013; 21:21131-47. [PMID: 24103988 DOI: 10.1364/oe.21.021131] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We present an experimental realization of coherent diffraction imaging in reflection geometry illuminating the sample with a laser driven high harmonic generation (HHG) based XUV source. After recording the diffraction pattern in reflection geometry, the data must be corrected before the image can be reconstructed with a hybrid-input-output (HIO) algorithm. In this paper we present a detailed investigation of sources of spoiling the reconstructed image due to the nonlinear momentum transfer, errors in estimating the angle of incidence on the sample, and distortions by placing the image off center in the computation grid. Finally we provide guidelines for the necessary parameters to realize a satisfactory reconstruction within a spatial resolution in the range of one micron for an imaging scheme with a numerical aperture NA < 0.03.
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