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Flenner S, Hagemann J, Wittwer F, Longo E, Kubec A, Rothkirch A, David C, Müller M, Greving I. Hard X-ray full-field nanoimaging using a direct photon-counting detector. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:390-399. [PMID: 36891852 PMCID: PMC10000802 DOI: 10.1107/s1600577522012103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Full-field X-ray nanoimaging is a widely used tool in a broad range of scientific areas. In particular, for low-absorbing biological or medical samples, phase contrast methods have to be considered. Three well established phase contrast methods at the nanoscale are transmission X-ray microscopy with Zernike phase contrast, near-field holography and near-field ptychography. The high spatial resolution, however, often comes with the drawback of a lower signal-to-noise ratio and significantly longer scan times, compared with microimaging. In order to tackle these challenges a single-photon-counting detector has been implemented at the nanoimaging endstation of the beamline P05 at PETRA III (DESY, Hamburg) operated by Helmholtz-Zentrum Hereon. Thanks to the long sample-to-detector distance available, spatial resolutions of below 100 nm were reached in all three presented nanoimaging techniques. This work shows that a single-photon-counting detector in combination with a long sample-to-detector distance allows one to increase the time resolution for in situ nanoimaging, while keeping a high signal-to-noise level.
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Affiliation(s)
- Silja Flenner
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Johannes Hagemann
- Center for X-ray and Nano Science – CXNS, Deutsches Elektronen-Synchrotron – DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Felix Wittwer
- Center for X-ray and Nano Science – CXNS, Deutsches Elektronen-Synchrotron – DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Elena Longo
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Adam Kubec
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - André Rothkirch
- Center for X-ray and Nano Science – CXNS, Deutsches Elektronen-Synchrotron – DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Christian David
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Martin Müller
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Imke Greving
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
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Marchesini S, Shapiro D, Maia FRNC. Introduction to the special issue on Ptychography: software and technical developments. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721002983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Du M, Kandel S, Deng J, Huang X, Demortiere A, Nguyen TT, Tucoulou R, De Andrade V, Jin Q, Jacobsen C. Adorym: a multi-platform generic X-ray image reconstruction framework based on automatic differentiation. OPTICS EXPRESS 2021; 29:10000-10035. [PMID: 33820138 PMCID: PMC8237934 DOI: 10.1364/oe.418296] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 05/09/2023]
Abstract
We describe and demonstrate an optimization-based X-ray image reconstruction framework called Adorym. Our framework provides a generic forward model, allowing one code framework to be used for a wide range of imaging methods ranging from near-field holography to fly-scan ptychographic tomography. By using automatic differentiation for optimization, Adorym has the flexibility to refine experimental parameters including probe positions, multiple hologram alignment, and object tilts. It is written with strong support for parallel processing, allowing large datasets to be processed on high-performance computing systems. We demonstrate its use on several experimental datasets to show improved image quality through parameter refinement.
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Affiliation(s)
- Ming Du
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Saugat Kandel
- Applied Physics Program, Northwestern University, Evanston, Illinois 60208, USA
| | - Junjing Deng
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Xiaojing Huang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Arnaud Demortiere
- Laboratoire de Réactivité et Chimie des Solides (LRCS), CNRS UMR 7314, Université de Picardie Jules Verne, Hub de l’Energie, 15 Rue Baudelocque, 80039 Amiens Cedex, France
| | - Tuan Tu Nguyen
- Laboratoire de Réactivité et Chimie des Solides (LRCS), CNRS UMR 7314, Université de Picardie Jules Verne, Hub de l’Energie, 15 Rue Baudelocque, 80039 Amiens Cedex, France
| | - Remi Tucoulou
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Vincent De Andrade
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Qiaoling Jin
- Department of Physics & Astronomy, Northwestern University, Evanston, Illinois 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
- Department of Physics & Astronomy, Northwestern University, Evanston, Illinois 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, USA
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Du M, Di ZW, Gürsoy D, Xian RP, Kozorovitskiy Y, Jacobsen C. Upscaling X-ray nanoimaging to macroscopic specimens. J Appl Crystallogr 2021; 54:386-401. [PMID: 33953650 PMCID: PMC8056767 DOI: 10.1107/s1600576721000194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/06/2021] [Indexed: 11/10/2022] Open
Abstract
Upscaling X-ray nanoimaging to macroscopic specimens has the potential for providing insights across multiple length scales, but its feasibility has long been an open question. By combining the imaging requirements and existing proof-of-principle examples in large-specimen preparation, data acquisition and reconstruction algorithms, the authors provide imaging time estimates for howX-ray nanoimaging can be scaled to macroscopic specimens. To arrive at this estimate, a phase contrast imaging model that includes plural scattering effects is used to calculate the required exposure and corresponding radiation dose. The coherent X-ray flux anticipated from upcoming diffraction-limited light sources is then considered. This imaging time estimation is in particular applied to the case of the connectomes of whole mouse brains. To image the connectome of the whole mouse brain, electron microscopy connectomics might require years, whereas optimized X-ray microscopy connectomics could reduce this to one week. Furthermore, this analysis points to challenges that need to be overcome (such as increased X-ray detector frame rate) and opportunities that advances in artificial-intelligence-based 'smart' scanning might provide. While the technical advances required are daunting, it is shown that X-ray microscopy is indeed potentially applicable to nanoimaging of millimetre- or even centimetre-size specimens.
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Affiliation(s)
- Ming Du
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zichao Wendy Di
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Doǧa Gürsoy
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208, USA
| | - R Patrick Xian
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Yevgenia Kozorovitskiy
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA.,Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
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Huang P, Du M, Hammer M, Miceli A, Jacobsen C. Fast digital lossy compression for X-ray ptychographic data. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:292-300. [PMID: 33399580 PMCID: PMC7842218 DOI: 10.1107/s1600577520013326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/05/2020] [Indexed: 05/02/2023]
Abstract
Increases in X-ray brightness from synchrotron light sources lead to a requirement for higher frame rates from hybrid pixel array detectors (HPADs), while also favoring charge integration over photon counting. However, transfer of the full uncompressed data will begin to constrain detector design, as well as limit the achievable continuous frame rate. Here a data compression scheme that is easy to implement in a HPAD's application-specific integrated circuit (ASIC) is described, and how different degrees of compression affect image quality in ptychography, a commonly employed coherent imaging method, is examined. Using adaptive encoding quantization, it is shown in simulations that one can digitize signals up to 16383 photons per pixel (corresponding to 14 bits of information) using only 8 or 9 bits for data transfer, with negligible effect on the reconstructed image.
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Affiliation(s)
- Panpan Huang
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - Ming Du
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Mike Hammer
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Antonino Miceli
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Chris Jacobsen
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Correspondence e-mail:
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