1
|
Direct retrieval of Zernike-based pupil functions using integrated diffractive deep neural networks. Nat Commun 2022; 13:7531. [PMID: 36476752 PMCID: PMC9729581 DOI: 10.1038/s41467-022-35349-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Retrieving the pupil phase of a beam path is a central problem for optical systems across scales, from telescopes, where the phase information allows for aberration correction, to the imaging of near-transparent biological samples in phase contrast microscopy. Current phase retrieval schemes rely on complex digital algorithms that process data acquired from precise wavefront sensors, reconstructing the optical phase information at great expense of computational resources. Here, we present a compact optical-electronic module based on multi-layered diffractive neural networks printed on imaging sensors, capable of directly retrieving Zernike-based pupil phase distributions from an incident point spread function. We demonstrate this concept numerically and experimentally, showing the direct pupil phase retrieval of superpositions of the first 14 Zernike polynomials. The integrability of the diffractive elements with CMOS sensors shows the potential for the direct extraction of the pupil phase information from a detector module without additional digital post-processing.
Collapse
|
2
|
Taphorn K, Busse M, Brantl J, Günther B, Diaz A, Holler M, Dierolf M, Mayr D, Pfeiffer F, Herzen J. X-ray Stain Localization with Near-Field Ptychographic Computed Tomography. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201723. [PMID: 35748171 PMCID: PMC9404393 DOI: 10.1002/advs.202201723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Although X-ray contrast agents offer specific characteristics in terms of targeting and attenuation, their accumulation in the tissue on a cellular level is usually not known and difficult to access, as it requires high resolution and sensitivity. Here, quantitative near-field ptychographic X-ray computed tomography is demonstrated to assess the location of X-ray stains at a resolution sufficient to identify intracellular structures by means of a basis material decomposition. On the example of two different X-ray stains, the nonspecific iodine potassium iodide, and eosin Y, which mostly interacts with proteins and peptides in the cell cytoplasm, the distribution of the stains within the cells in murine kidney samples is assessed and compared to unstained samples with similar structural features. Quantitative nanoscopic stain concentrations are in good agreement with dual-energy micro computed tomography measurements, the state-of-the-art modality for material-selective imaging. The presented approach can be applied to a variety of X-ray stains advancing the development of X-ray contrast agents.
Collapse
Affiliation(s)
- Kirsten Taphorn
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
| | - Madleen Busse
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
| | - Johannes Brantl
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
| | - Benedikt Günther
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
| | - Ana Diaz
- Paul Scherrer InstituteVilligen5232Switzerland
| | | | - Martin Dierolf
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
| | - Doris Mayr
- Institute of PathologyLudwig‐Maximilians‐University80337MunichGermany
| | - Franz Pfeiffer
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
- Department of Diagnostic and Interventional RadiologySchool of Medicine & Klinikum rechts der IsarTechnical University of Munich81675MünchenGermany
- Institute for Advanced StudyTechnical University of Munich85748GarchingGermany
| | - Julia Herzen
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
| |
Collapse
|
3
|
Eschen W, Loetgering L, Schuster V, Klas R, Kirsche A, Berthold L, Steinert M, Pertsch T, Gross H, Krause M, Limpert J, Rothhardt J. Material-specific high-resolution table-top extreme ultraviolet microscopy. LIGHT: SCIENCE & APPLICATIONS 2022; 11:117. [PMID: 35487910 PMCID: PMC9054792 DOI: 10.1038/s41377-022-00797-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 05/25/2023]
Abstract
AbstractMicroscopy with extreme ultraviolet (EUV) radiation holds promise for high-resolution imaging with excellent material contrast, due to the short wavelength and numerous element-specific absorption edges available in this spectral range. At the same time, EUV radiation has significantly larger penetration depths than electrons. It thus enables a nano-scale view into complex three-dimensional structures that are important for material science, semiconductor metrology, and next-generation nano-devices. Here, we present high-resolution and material-specific microscopy at 13.5 nm wavelength. We combine a highly stable, high photon-flux, table-top EUV source with an interferometrically stabilized ptychography setup. By utilizing structured EUV illumination, we overcome the limitations of conventional EUV focusing optics and demonstrate high-resolution microscopy at a half-pitch lateral resolution of 16 nm. Moreover, we propose mixed-state orthogonal probe relaxation ptychography, enabling robust phase-contrast imaging over wide fields of view and long acquisition times. In this way, the complex transmission of an integrated circuit is precisely reconstructed, allowing for the classification of the material composition of mesoscopic semiconductor systems.
Collapse
|
4
|
Lo YH, Liao CT, Zhou J, Rana A, Bevis CS, Gui G, Enders B, Cannon KM, Yu YS, Celestre R, Nowrouzi K, Shapiro D, Kapteyn H, Falcone R, Bennett C, Murnane M, Miao J. Multimodal x-ray and electron microscopy of the Allende meteorite. SCIENCE ADVANCES 2019; 5:eaax3009. [PMID: 31555739 PMCID: PMC6754224 DOI: 10.1126/sciadv.aax3009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
Multimodal microscopy that combines complementary nanoscale imaging techniques is critical for extracting comprehensive chemical, structural, and functional information, particularly for heterogeneous samples. X-ray microscopy can achieve high-resolution imaging of bulk materials with chemical, magnetic, electronic, and bond orientation contrast, while electron microscopy provides atomic-scale spatial resolution with quantitative elemental composition. Here, we combine x-ray ptychography and scanning transmission x-ray spectromicroscopy with three-dimensional energy-dispersive spectroscopy and electron tomography to perform structural and chemical mapping of an Allende meteorite particle with 15-nm spatial resolution. We use textural and quantitative elemental information to infer the mineral composition and discuss potential processes that occurred before or after accretion. We anticipate that correlative x-ray and electron microscopy overcome the limitations of individual imaging modalities and open up a route to future multiscale nondestructive microscopies of complex functional materials and biological systems.
Collapse
Affiliation(s)
- 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
| | - Chen-Ting Liao
- JILA and Department of Physics, University of Colorado and National Institute of Standards and Technology (NIST), Boulder, CO 80309, USA
| | - Jihan Zhou
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Arjun Rana
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Charles S. Bevis
- JILA and Department of Physics, University of Colorado and National Institute of Standards and Technology (NIST), Boulder, CO 80309, USA
| | - Guan Gui
- JILA and Department of Physics, University of Colorado and National Institute of Standards and Technology (NIST), Boulder, CO 80309, USA
| | - Bjoern Enders
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kevin M. Cannon
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA
| | - Young-Sang Yu
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Richard Celestre
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kasra Nowrouzi
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Henry Kapteyn
- JILA and Department of Physics, University of Colorado and National Institute of Standards and Technology (NIST), Boulder, CO 80309, USA
| | - Roger Falcone
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chris Bennett
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA
| | - Margaret Murnane
- JILA and Department of Physics, University of Colorado and National Institute of Standards and Technology (NIST), Boulder, CO 80309, USA
| | - Jianwei Miao
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
5
|
Nave C. A comparison of absorption and phase contrast for X-ray imaging of biological cells. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1490-1504. [PMID: 30179189 PMCID: PMC6140389 DOI: 10.1107/s1600577518009566] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 07/04/2018] [Indexed: 05/04/2023]
Abstract
X-ray imaging allows biological cells to be examined at a higher resolution than possible with visible light and without some of the preparation difficulties associated with electron microscopy of thick samples. The most used and developed technique is absorption contrast imaging in the water window which exploits the contrast between carbon and oxygen at an energy of around 500 eV. A variety of phase contrast techniques are also being developed. In general these operate at a higher energy, enabling thicker cells to be examined and, in some cases, can be combined with X-ray fluorescence imaging to locate specific metals. The various methods are based on the differences between the complex refractive indices of the cellular components and the surrounding cytosol or nucleosol, the fluids present in the cellular cytoplasm and nucleus. The refractive indices can be calculated from the atomic composition and density of the components. These in turn can be obtained from published measurements using techniques such as chemical analysis, scanning electron microscopy and X-ray imaging at selected energies. As examples, the refractive indices of heterochromatin, inner mitochondrial membranes, the neutral core of lipid droplets, starch granules, cytosol and nucleosol are calculated. The refractive index calculations enable the required doses and fluences to be obtained to provide images with sufficient statistical significance, for X-ray energies between 200 and 4000 eV. The statistical significance (e.g. the Rose criterion) for various requirements is discussed. The calculations reveal why some cellular components are more visible by absorption contrast and why much greater exposure times are required to see some cellular components. A comparison of phase contrast as a function of photon energy with absorption contrast in the water window is provided and it is shown that much higher doses are generally required for the phase contrast measurements. This particularly applies to those components with a high carbon content but with a mass density similar to the surrounding cytosol or nucleosol. The results provide guidance for the most appropriate conditions for X-ray imaging of individual cellular components within cells of various thicknesses.
Collapse
Affiliation(s)
- Colin Nave
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Correspondence e-mail:
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Yan H, Nazaretski E, Lauer K, Huang X, Wagner U, Rau C, Yusuf M, Robinson I, Kalbfleisch S, Li L, Bouet N, Zhou J, Conley R, Chu YS. Multimodality hard-x-ray imaging of a chromosome with nanoscale spatial resolution. Sci Rep 2016; 6:20112. [PMID: 26846188 PMCID: PMC4742846 DOI: 10.1038/srep20112] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/29/2015] [Indexed: 11/17/2022] Open
Abstract
We developed a scanning hard x-ray microscope using a new class of x-ray nano-focusing optic called a multilayer Laue lens and imaged a chromosome with nanoscale spatial resolution. The combination of the hard x-ray’s superior penetration power, high sensitivity to elemental composition, high spatial-resolution and quantitative analysis creates a unique tool with capabilities that other microscopy techniques cannot provide. Using this microscope, we simultaneously obtained absorption-, phase-, and fluorescence-contrast images of Pt-stained human chromosome samples. The high spatial-resolution of the microscope and its multi-modality imaging capabilities enabled us to observe the internal ultra-structures of a thick chromosome without sectioning it.
Collapse
Affiliation(s)
- Hanfei Yan
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Evgeny Nazaretski
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Kenneth Lauer
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Xiaojing Huang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Ulrich Wagner
- Diamond Light Source Ltd, Didcot, Oxfordshire, OX11 0DE, UK
| | - Christoph Rau
- Diamond Light Source Ltd, Didcot, Oxfordshire, OX11 0DE, UK
| | - Mohammed Yusuf
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.,Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.,Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Sebastian Kalbfleisch
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Li Li
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nathalie Bouet
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Juan Zhou
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Ray Conley
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA.,Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Yong S Chu
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| |
Collapse
|
8
|
Diaz A, Malkova B, Holler M, Guizar-Sicairos M, Lima E, Panneels V, Pigino G, Bittermann AG, Wettstein L, Tomizaki T, Bunk O, Schertler G, Ishikawa T, Wepf R, Menzel A. Three-dimensional mass density mapping of cellular ultrastructure by ptychographic X-ray nanotomography. J Struct Biol 2015; 192:461-469. [DOI: 10.1016/j.jsb.2015.10.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 10/06/2015] [Accepted: 10/10/2015] [Indexed: 11/16/2022]
|