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Burchert JP, Frohn J, Rölleke U, Bruns H, Yu B, Gleber SC, Stange R, Busse M, Osterhoff M, Salditt T, Köster S. X-ray phase-contrast tomography of cells manipulated with an optical stretcher. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:923-935. [PMID: 38861370 PMCID: PMC11226146 DOI: 10.1107/s1600577524003618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/21/2024] [Indexed: 06/13/2024]
Abstract
X-rays can penetrate deeply into biological cells and thus allow for examination of their internal structures with high spatial resolution. In this study, X-ray phase-contrast imaging and tomography is combined with an X-ray-compatible optical stretcher and microfluidic sample delivery. Using this setup, individual cells can be kept in suspension while they are examined with the X-ray beam at a synchrotron. From the recorded holograms, 2D phase shift images that are proportional to the projected local electron density of the investigated cell can be calculated. From the tomographic reconstruction of multiple such projections the 3D electron density can be obtained. The cells can thus be studied in a hydrated or even living state, thus avoiding artifacts from freezing, drying or embedding, and can in principle also be subjected to different sample environments or mechanical strains. This combination of techniques is applied to living as well as fixed and stained NIH3T3 mouse fibroblasts and the effect of the beam energy on the phase shifts is investigated. Furthermore, a 3D algebraic reconstruction scheme and a dedicated mathematical description is used to follow the motion of the trapped cells in the optical stretcher for multiple rotations.
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Affiliation(s)
- Jan-Philipp Burchert
- Institute for X-ray PhysicsUniversity of GöttingenFriedrich-Hund-Platz 137077GöttingenGermany
- Cluster of Excellence Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC)University of GöttingenGermany
| | - Jasper Frohn
- Institute for X-ray PhysicsUniversity of GöttingenFriedrich-Hund-Platz 137077GöttingenGermany
| | - Ulrike Rölleke
- Institute for X-ray PhysicsUniversity of GöttingenFriedrich-Hund-Platz 137077GöttingenGermany
| | - Hendrik Bruns
- Institute for X-ray PhysicsUniversity of GöttingenFriedrich-Hund-Platz 137077GöttingenGermany
| | - Boram Yu
- Institute for X-ray PhysicsUniversity of GöttingenFriedrich-Hund-Platz 137077GöttingenGermany
| | - Sophie-Charlotte Gleber
- Institute for X-ray PhysicsUniversity of GöttingenFriedrich-Hund-Platz 137077GöttingenGermany
| | | | - Madleen Busse
- Biomedical Physics, School of ScienceTechnical University MunichBoltzmannstraße 1185748GarchingGermany
- Munich Institute of Biomedical EngineeringTechnical University MunichBoltzmannstraße 1185748GarchingGermany
| | - Markus Osterhoff
- Institute for X-ray PhysicsUniversity of GöttingenFriedrich-Hund-Platz 137077GöttingenGermany
| | - Tim Salditt
- Institute for X-ray PhysicsUniversity of GöttingenFriedrich-Hund-Platz 137077GöttingenGermany
- Cluster of Excellence Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC)University of GöttingenGermany
| | - Sarah Köster
- Institute for X-ray PhysicsUniversity of GöttingenFriedrich-Hund-Platz 137077GöttingenGermany
- Cluster of Excellence Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC)University of GöttingenGermany
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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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Schmollinger S, Chen S, Merchant SS. Quantitative elemental imaging in eukaryotic algae. Metallomics 2023; 15:mfad025. [PMID: 37186252 PMCID: PMC10209819 DOI: 10.1093/mtomcs/mfad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/03/2023] [Indexed: 05/17/2023]
Abstract
All organisms, fundamentally, are made from the same raw material, namely the elements of the periodic table. Biochemical diversity is achieved by how these elements are utilized, for what purpose, and in which physical location. Determining elemental distributions, especially those of trace elements that facilitate metabolism as cofactors in the active centers of essential enzymes, can determine the state of metabolism, the nutritional status, or the developmental stage of an organism. Photosynthetic eukaryotes, especially algae, are excellent subjects for quantitative analysis of elemental distribution. These microbes utilize unique metabolic pathways that require various trace nutrients at their core to enable their operation. Photosynthetic microbes also have important environmental roles as primary producers in habitats with limited nutrient supplies or toxin contaminations. Accordingly, photosynthetic eukaryotes are of great interest for biotechnological exploitation, carbon sequestration, and bioremediation, with many of the applications involving various trace elements and consequently affecting their quota and intracellular distribution. A number of diverse applications were developed for elemental imaging, allowing subcellular resolution, with X-ray fluorescence microscopy (XFM, XRF) being at the forefront, enabling quantitative descriptions of intact cells in a non-destructive method. This Tutorial Review summarizes the workflow of a quantitative, single-cell elemental distribution analysis of a eukaryotic alga using XFM.
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Affiliation(s)
- Stefan Schmollinger
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Si Chen
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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4
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Vacek E, Preissner C, Deng J, Jacobsen C. Fast scanning in x-ray microscopy: the effects of offset in the central stop position. APPLIED OPTICS 2022; 61:6811-6818. [PMID: 36255769 DOI: 10.1364/ao.469319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 06/16/2023]
Abstract
Scanning of lightweight circular diffractive optics, separate from central stops and apertures, is emerging as an approach to exploit advances in synchrotron x-ray sources. We consider the effects in a scanning microscope of offsets between the optic and its central stop and find that scan ranges of up to about half the diameter of the optic are possible with only about a 10% increase in the focal spot width. For large scanning ranges, we present criteria for the working distance between the last aperture and the specimen to be imaged.
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5
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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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6
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Nanometer-Resolution Imaging of Living Cells Using Soft X-ray Contact Microscopy. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12147030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Soft X-ray microscopy is a powerful technique for imaging cells with nanometer resolution in their native state without chemical fixation, staining, or sectioning. The studies performed in several laboratories have demonstrated the potential of applying this technique for imaging the internal structures of intact cells. However, it is currently used mainly on synchrotrons with restricted access. Moreover, the operation of these instruments and the associated sample-preparation protocols require interdisciplinary and highly specialized personnel, limiting their wide application in practice. This is why soft X-ray microscopy is not commonly used in biological laboratories as an imaging tool. Thus, a laboratory-based and user-friendly soft X-ray contact microscope would facilitate the work of biologists. A compact, desk-top laboratory setup for soft X-ray contact microscopy (SXCM) based on a laser-plasma soft X-ray source, which can be used in any biological laboratory, together with several applications for biological imaging, are described. Moreover, the perspectives of the correlation of SXCM with other super-resolution imaging techniques based on the current literature are discussed.
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7
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Riazanski V, Mauleon G, Zimnicka AM, Chen S, Nelson DJ. Phagosomal chloride dynamics in the alveolar macrophage. iScience 2022; 25:103636. [PMID: 35024579 PMCID: PMC8733233 DOI: 10.1016/j.isci.2021.103636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 10/11/2021] [Accepted: 12/14/2021] [Indexed: 12/04/2022] Open
Abstract
Acidification in intracellular organelles is tightly linked to the influx of Cl- counteracting proton translocation by the electrogenic V-ATPase. We quantified the dynamics of Cl- transfer accompanying cargo incorporation into single phagosomes in alveolar macrophages (AMs). Phagosomal Cl- concentration and acidification magnitude were followed in real time with maximal acidification achieved at levels of approximately 200 mM. Live cell confocal microscopy verified that phagosomal Cl- influx utilized predominantly the Cl- channel CFTR. Relative levels of elemental chlorine (Cl) in hard X-ray fluorescence microprobe (XFM) analysis within single phagosomes validated the increase in Cl- content. XFM revealed the complex interplay between elemental K content inside the phagosome and changes in Cl- during phagosomal particle uptake. Cl- -dependent changes in phagosomal membrane potential were obtained using second harmonic generation (SHG) microscopy. These studies provide a mechanistic insight for screening studies in drug development targeting pulmonary inflammatory disease.
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Affiliation(s)
- Vladimir Riazanski
- The University of Chicago, Department of Pharmacological and Physiological Sciences, 947 E. 58th Street, MC 0926, Chicago, IL 60637, USA
| | - Gerardo Mauleon
- The University of Chicago, Department of Pharmacological and Physiological Sciences, 947 E. 58th Street, MC 0926, Chicago, IL 60637, USA
| | - Adriana M. Zimnicka
- The University of Chicago, Department of Pharmacological and Physiological Sciences, 947 E. 58th Street, MC 0926, Chicago, IL 60637, USA
| | - Si Chen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Deborah J. Nelson
- The University of Chicago, Department of Pharmacological and Physiological Sciences, 947 E. 58th Street, MC 0926, Chicago, IL 60637, USA
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8
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Chevrier DM, Cerdá-Doñate E, Park Y, Cacho-Nerin F, Gomez‐Gonzalez M, Uebe R, Faivre D. Synchrotron‐Based Nano‐X‐Ray Absorption Near‐Edge Structure Revealing Intracellular Heterogeneity of Iron Species in Magnetotactic Bacteria. SMALL SCIENCE 2021. [DOI: 10.1002/smsc.202100089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Daniel M. Chevrier
- CNRS CEA BIAM Aix-Marseille Université 13108 Saint-Paul-lez-Durance France
- Department of Biomaterials Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
| | - Elisa Cerdá-Doñate
- Department of Biomaterials Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
| | - Yeseul Park
- CNRS CEA BIAM Aix-Marseille Université 13108 Saint-Paul-lez-Durance France
| | | | | | - René Uebe
- Department of Microbiology University of Bayreuth 95440 Bayreuth Germany
| | - Damien Faivre
- CNRS CEA BIAM Aix-Marseille Université 13108 Saint-Paul-lez-Durance France
- Department of Biomaterials Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
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9
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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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10
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Wang B, He Z, Zhang F. Coherent modulation imaging using unknown modulators. OPTICS EXPRESS 2021; 29:30035-30044. [PMID: 34614735 DOI: 10.1364/oe.434111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Coherent modulation imaging (CMI) is an effective lensless diffraction imaging method with fast algorithmic convergence and high robustness to data defects. In the reported algorithms for CMI, one important requirement is that the modulator function need to be known a priori; and an additional step for the modulator characterization is required to be carried out in advance by other methods, such as ptychography, which could be cumbersome in practice. Here, we propose an improved algorithm that allows for the transmission function of a completely unknown modulator to be recovered during the same iterative process of image reconstruction. We have verified the method in both simulations and optical experiments. This improvement would turn CMI into a more practical and standalone technique for broader applications in biology and materials science.
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11
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Soltau J, Chayanun L, Lyubomirskiy M, Wallentin J, Osterhoff M. Off-axis multilayer zone plate with 16 nm × 28 nm focus for high-resolution X-ray beam induced current imaging. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1573-1582. [PMID: 34475304 PMCID: PMC8415331 DOI: 10.1107/s1600577521006159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Using multilayer zone plates (MZPs) as two-dimensional optics, focal spot sizes of less than 10 nm can be achieved, as we show here with a focus of 8.4 nm × 9.6 nm, but the need for order-sorting apertures prohibits practical working distances. To overcome this issue, here an off-axis illumination of a circular MZP is introduced to trade off between working distance and focal spot size. By this, the working distance between order-sorting aperture and sample can be more than doubled. Exploiting a 2D focus of 16 nm × 28 nm, real-space 2D mapping of local electric fields and charge carrier recombination using X-ray beam induced current in a single InP nanowire is demonstrated. Simulations show that a dedicated off-axis MZP can reach sub-10 nm focusing combined with reasonable working distances and low background, which could be used for in operando imaging of composition, carrier collection and strain in nanostructured devices.
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Affiliation(s)
- Jakob Soltau
- Institute for X-ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Lert Chayanun
- Synchrotron Radiation Research and NanoLund, Lund University, Box 118, 22100 Lund, Sweden
| | | | - Jesper Wallentin
- Synchrotron Radiation Research and NanoLund, Lund University, Box 118, 22100 Lund, Sweden
| | - Markus Osterhoff
- Institute for X-ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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12
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Single-cell visualization and quantification of trace metals in Chlamydomonas lysosome-related organelles. Proc Natl Acad Sci U S A 2021; 118:2026811118. [PMID: 33879572 DOI: 10.1073/pnas.2026811118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The acidocalcisome is an acidic organelle in the cytosol of eukaryotes, defined by its low pH and high calcium and polyphosphate content. It is visualized as an electron-dense object by transmission electron microscopy (TEM) or described with mass spectrometry (MS)-based imaging techniques or multimodal X-ray fluorescence microscopy (XFM) based on its unique elemental composition. Compared with MS-based imaging techniques, XFM offers the additional advantage of absolute quantification of trace metal content, since sectioning of the cell is not required and metabolic states can be preserved rapidly by either vitrification or chemical fixation. We employed XFM in Chlamydomonas reinhardtii to determine single-cell and organelle trace metal quotas within algal cells in situations of trace metal overaccumulation (Fe and Cu). We found up to 70% of the cellular Cu and 80% of Fe sequestered in acidocalcisomes in these conditions and identified two distinct populations of acidocalcisomes, defined by their unique trace elemental makeup. We utilized the vtc1 mutant, defective in polyphosphate synthesis and failing to accumulate Ca, to show that Fe sequestration is not dependent on either. Finally, quantitation of the Fe and Cu contents of individual cells and compartments via XFM, over a range of cellular metal quotas created by nutritional and genetic perturbations, indicated excellent correlation with bulk data from corresponding cell cultures, establishing a framework to distinguish the nutritional status of single cells.
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13
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Villanueva-Perez P, Fleckenstein H, Prasciolu M, Murray KT, Domaracký M, Gregorič K, Mariani V, Gelisio L, Kuhn M, Hannappel J, Yefanov O, Ivanov N, Sarrou I, Pennicard D, Becker J, von Zimmermann M, Gutowski O, Dippel AC, Chapman HN, Bajt S. Scanning Compton X-ray microscopy. OPTICS LETTERS 2021; 46:1920-1923. [PMID: 33857104 DOI: 10.1364/ol.421232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
X-ray microscopy offers the opportunity to image biological and radiosensitive materials without special sample preparations, bridging optical and electron microscopy capabilities. However, the performance of such microscopes, when imaging radiosensitive samples, is not limited by their intrinsic resolution, but by the radiation damage induced on such samples. Here, we demonstrate a novel, to the best of our knowledge, radio-efficient microscope, scanning Compton X-ray microscopy (SCXM), which uses coherently and incoherently (Compton) scattered photons to minimize the deposited energy per unit of mass for a given imaging signal. We implemented SCXM, using lenses capable of efficiently focusing 60 keV X-ray photons into the sub-micrometer scale, and probe its radio-efficient capabilities. SCXM, when implemented in high-energy diffraction-limited storage rings, e.g., European Synchrotron Radiation Facility Extremely Brilliant Source and PETRA IV, will open the opportunity to explore the nanoscale of unstained, unsectioned, and undamaged radiosensitive materials.
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14
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Wang J, Ilyas S. Targeting the tumor microenvironment in cholangiocarcinoma: implications for therapy. Expert Opin Investig Drugs 2021; 30:429-438. [PMID: 33322977 PMCID: PMC8096665 DOI: 10.1080/13543784.2021.1865308] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/14/2020] [Indexed: 02/08/2023]
Abstract
Introduction: Cholangiocarcinomas (CCAs) are biliary epithelial tumors with rising incidence over the past 3 decades. Early diagnosis of CCAs remains a significant challenge and the majority of patients present at an advanced stage. CCAs are heterogeneous tumors and currently available standard systemic therapy options are of limited effectiveness. Immune checkpoint inhibition (ICI) has transformed cancer therapy across a spectrum of malignancies. However, the response rate to ICI has been relatively disappointing in CCAs owing to its desmoplastic tumor microenvironment (TME).Areas covered: Tumor microenvironment of CCAs consists of innate and adaptive cells, stromal cells, and extracellular components (cytokines, chemokines, exosomes, etc.). This intricate microenvironment has multiple immunosuppressive elements that promote tumor cell survival and therapeutic resistance. Accordingly, there is a need for the development of effective therapeutic strategies that target the TME. Herein, we review the components of the CCA TME, and potential therapies targeting the CCA TME.Expert opinion: CCAs are desmoplastic tumors with a dense tumor microenvironment. An enhanced understanding of the various components of the CCA TME is essential in the effort to develop novel biomarkers for patient stratification as well as combination therapeutic strategies that target the tumor plus the TME.
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Affiliation(s)
- Juan Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Sumera Ilyas
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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15
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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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16
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Tran HT, Tsai EHR, Lewis AJ, Moors T, Bol JGJM, Rostami I, Diaz A, Jonker AJ, Guizar-Sicairos M, Raabe J, Stahlberg H, van de Berg WDJ, Holler M, Shahmoradian SH. Alterations in Sub-Axonal Architecture Between Normal Aging and Parkinson's Diseased Human Brains Using Label-Free Cryogenic X-ray Nanotomography. Front Neurosci 2020; 14:570019. [PMID: 33324142 PMCID: PMC7724048 DOI: 10.3389/fnins.2020.570019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/14/2020] [Indexed: 01/25/2023] Open
Abstract
Gaining insight to pathologically relevant processes in continuous volumes of unstained brain tissue is important for a better understanding of neurological diseases. Many pathological processes in neurodegenerative disorders affect myelinated axons, which are a critical part of the neuronal circuitry. Cryo ptychographic X-ray computed tomography in the multi-keV energy range is an emerging technology providing phase contrast at high sensitivity, allowing label-free and non-destructive three dimensional imaging of large continuous volumes of tissue, currently spanning up to 400,000 μm3. This aspect makes the technique especially attractive for imaging complex biological material, especially neuronal tissues, in combination with downstream optical or electron microscopy techniques. A further advantage is that dehydration, additional contrast staining, and destructive sectioning/milling are not required for imaging. We have developed a pipeline for cryo ptychographic X-ray tomography of relatively large, hydrated and unstained biological tissue volumes beyond what is typical for the X-ray imaging, using human brain tissue and combining the technique with complementary methods. We present four imaged volumes of a Parkinson's diseased human brain and five volumes from a non-diseased control human brain using cryo ptychographic X-ray tomography. In both cases, we distinguish neuromelanin-containing neurons, lipid and melanic pigment, blood vessels and red blood cells, and nuclei of other brain cells. In the diseased sample, we observed several swellings containing dense granular material resembling clustered vesicles between the myelin sheaths arising from the cytoplasm of the parent oligodendrocyte, rather than the axoplasm. We further investigated the pathological relevance of such swollen axons in adjacent tissue sections by immunofluorescence microscopy for phosphorylated alpha-synuclein combined with multispectral imaging. Since cryo ptychographic X-ray tomography is non-destructive, the large dataset volumes were used to guide further investigation of such swollen axons by correlative electron microscopy and immunogold labeling post X-ray imaging, a possibility demonstrated for the first time. Interestingly, we find that protein antigenicity and ultrastructure of the tissue are preserved after the X-ray measurement. As many pathological processes in neurodegeneration affect myelinated axons, our work sets an unprecedented foundation for studies addressing axonal integrity and disease-related changes in unstained brain tissues.
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Affiliation(s)
| | | | - Amanda J. Lewis
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Tim Moors
- Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - J. G. J. M. Bol
- Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | - Ana Diaz
- Paul Scherrer Institut, Villigen, Switzerland
| | - Allert J. Jonker
- Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | - Joerg Raabe
- Paul Scherrer Institut, Villigen, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Wilma D. J. van de Berg
- Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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17
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Genoud S, Jones MWM, Trist BG, Deng J, Chen S, Hare DJ, Double KL. Simultaneous structural and elemental nano-imaging of human brain tissue. Chem Sci 2020; 11:8919-8927. [PMID: 34123146 PMCID: PMC8163372 DOI: 10.1039/d0sc02844d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Examining chemical and structural characteristics of micro-features in complex tissue matrices is essential for understanding biological systems. Advances in multimodal chemical and structural imaging using synchrotron radiation have overcome many issues in correlative imaging, enabling the characterization of distinct microfeatures at nanoscale resolution in ex vivo tissues. We present a nanoscale imaging method that pairs X-ray ptychography and X-ray fluorescence microscopy (XFM) to simultaneously examine structural features and quantify elemental content of microfeatures in complex ex vivo tissues. We examined the neuropathological microfeatures Lewy bodies, aggregations of superoxide dismutase 1 (SOD1) and neuromelanin in human post-mortem Parkinson's disease tissue. Although biometals play essential roles in normal neuronal biochemistry, their dyshomeostasis is implicated in Parkinson's disease aetiology. Here we show that Lewy bodies and SOD1 aggregates have distinct elemental fingerprints yet are similar in structure, whilst neuromelanin exhibits different elemental composition and a distinct, disordered structure. The unique approach we describe is applicable to the structural and chemical characterization of a wide range of complex biological tissues at previously unprecedented levels of detail. Structural and chemical characterisation of microfeatures in unadulterated Parkinson's disease brain tissue using synchrotron nanoscale XFM and ptychography.![]()
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Affiliation(s)
- Sian Genoud
- Brain and Mind Centre and Discipline of Pharmacology, The University of Sydney Camperdown NSW 2050 Australia
| | - Michael W M Jones
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology Brisbane QLD 4000 Australia
| | - Benjamin Guy Trist
- Brain and Mind Centre and Discipline of Pharmacology, The University of Sydney Camperdown NSW 2050 Australia
| | - Junjing Deng
- Advanced Photon Source, Argonne National Laboratory Lemont IL 60439 USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory Lemont IL 60439 USA
| | - Dominic James Hare
- Brain and Mind Centre and Discipline of Pharmacology, The University of Sydney Camperdown NSW 2050 Australia .,School of Biosciences, Department of Clinical Pathology, The University of Melbourne Parkville VIC 3010 Australia .,Atomic Medicine Initiative, University of Technology Sydney NSW 2007 Australia
| | - Kay L Double
- Brain and Mind Centre and Discipline of Pharmacology, The University of Sydney Camperdown NSW 2050 Australia
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18
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Nano-imaging trace elements at organelle levels in substantia nigra overexpressing α-synuclein to model Parkinson's disease. Commun Biol 2020; 3:364. [PMID: 32647232 PMCID: PMC7347932 DOI: 10.1038/s42003-020-1084-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 06/18/2020] [Indexed: 12/17/2022] Open
Abstract
Sub-cellular trace element quantifications of nano-heterogeneities in brain tissues offer unprecedented ways to explore at elemental level the interplay between cellular compartments in neurodegenerative pathologies. We designed a quasi-correlative method for analytical nanoimaging of the substantia nigra, based on transmission electron microscopy and synchrotron X-ray fluorescence. It combines ultrastructural identifications of cellular compartments and trace element nanoimaging near detection limits, for increased signal-to-noise ratios. Elemental composition of different organelles is compared to cytoplasmic and nuclear compartments in dopaminergic neurons of rat substantia nigra. They exhibit 150–460 ppm of Fe, with P/Zn/Fe-rich nucleoli in a P/S-depleted nuclear matrix and Ca-rich rough endoplasmic reticula. Cytoplasm analysis displays sub-micron Fe/S-rich granules, including lipofuscin. Following AAV-mediated overexpression of α-synuclein protein associated with Parkinson’s disease, these granules shift towards higher Fe concentrations. This effect advocates for metal (Fe) dyshomeostasis in discrete cytoplasmic regions, illustrating the use of this method to explore neuronal dysfunction in brain diseases. Lemelle et al. describe the use of TEM and synchrotron X-ray fluorescence for quasi-correlative nanoimaging and sub-cellular trace element quantification of rat brain tissue. They further observe elemental (iron and sulfur) dyshomeostasis in cytoplasmic granules when overexpressing α-synuclein protein associated with Parkinson’s disease, demonstrating the usefulness of this method to further explore dysfunctions at organelle levels in brain diseases.
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19
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Du M, Gürsoy D, Jacobsen C. Near, far, wherever you are: simulations on the dose efficiency of holographic and ptychographic coherent imaging. J Appl Crystallogr 2020; 53:748-759. [PMID: 32684890 PMCID: PMC7312132 DOI: 10.1107/s1600576720005816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 04/27/2020] [Indexed: 02/03/2023] Open
Abstract
Different studies in X-ray microscopy have arrived at conflicting conclusions about the dose efficiency of imaging modes involving the recording of intensity distributions in the near (Fresnel regime) or far (Fraunhofer regime) field downstream of a specimen. A numerical study is presented on the dose efficiency of near-field holography, near-field ptychography and far-field ptychography, where ptychography involves multiple overlapping finite-sized illumination positions. Unlike what has been reported for coherent diffraction imaging, which involves recording a single far-field diffraction pattern, it is found that all three methods offer similar image quality when using the same fluence on the specimen, with far-field ptychography offering slightly better spatial resolution and a lower mean error. These results support the concept that (if the experiment and image reconstruction are done properly) the sample can be near or far; wherever you are, photon fluence on the specimen sets one limit to spatial resolution.
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Affiliation(s)
- Ming Du
- Advanced Photon Source, 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
| | - 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
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20
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De Caro L, Scattarella F, Altamura D, Arciniegas MP, Siliqi D, Manna L, Giannini C. X-ray ptychographic mode of self-assembled CdSe/CdS octapod-shaped nanocrystals in thick polymers. J Appl Crystallogr 2020; 53:741-747. [PMID: 32684889 PMCID: PMC7312151 DOI: 10.1107/s160057672000583x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 04/27/2020] [Indexed: 11/10/2022] Open
Abstract
This work describes the application of X-ray ptychography for the inspection of complex assemblies of highly anisotropic nanocrystals embedded in a thick polymer matrix. More specifically, this case deals with CdSe/CdS octapods, with pod length L = 39 ± 2 nm and pod diameter D = 12 ± 2 nm, dispersed in free-standing thick films (24 ± 4 µm) of polymethyl methacrylate and polystyrene, with different molecular weights. Ptychography is the only imaging method available to date that can be used to study architectures made by these types of nanocrystals in thick polymeric films, as any other alternative direct method, such as scanning/transmission electron microscopy, can be definitively ruled out as a result of the large thickness of the free-standing films. The electron density maps of the investigated samples are reconstructed by combining iterative difference map algorithms and a maximum likelihood optimization algorithm. In addition, post image processing techniques are applied to both reduce noise and provide a better visualization of the material morphological details. Through this process, at a final resolution of 27 nm, the reconstructed maps allow us to visualize the intricate network of octapods inside the polymeric matrices.
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Affiliation(s)
- Liberato De Caro
- Istituto di Cristallografia, CNR, via Amendola 122/O, Bari, Italy
| | | | - Davide Altamura
- Istituto di Cristallografia, CNR, via Amendola 122/O, Bari, Italy
| | - Milena P. Arciniegas
- Nanochemistry Department, Istituto Italiano di Tecnologia, via Morego 30, Genova, Italy
| | - Dritan Siliqi
- Istituto di Cristallografia, CNR, via Amendola 122/O, Bari, Italy
| | - Liberato Manna
- Nanochemistry Department, Istituto Italiano di Tecnologia, via Morego 30, Genova, Italy
| | - Cinzia Giannini
- Istituto di Cristallografia, CNR, via Amendola 122/O, Bari, Italy
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21
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Nave C. The achievable resolution for X-ray imaging of cells and other soft biological material. IUCRJ 2020; 7:393-403. [PMID: 32431823 PMCID: PMC7201285 DOI: 10.1107/s2052252520002262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/18/2020] [Indexed: 06/11/2023]
Abstract
X-ray imaging of soft materials is often difficult because of the low contrast of the components. This particularly applies to frozen hydrated biological cells where the feature of interest can have a similar density to the surroundings. As a consequence, a high dose is often required to achieve the desired resolution. However, the maximum dose that a specimen can tolerate is limited by radiation damage. Results from 3D coherent diffraction imaging (CDI) of frozen hydrated specimens have given resolutions of ∼80 nm compared with the expected resolution of 10 nm predicted from theoretical considerations for identifying a protein embedded in water. Possible explanations for this include the inapplicability of the dose-fractionation theorem, the difficulty of phase determination, an overall object-size dependence on the required fluence and dose, a low contrast within the biological cell, insufficient exposure, and a variety of practical difficulties such as scattering from surrounding material. A recent article [Villaneuva-Perez et al. (2018), Optica, 5, 450-457] concluded that imaging by Compton scattering gave a large dose advantage compared with CDI because of the object-size dependence for CDI. An object-size dependence would severely limit the applicability of CDI and perhaps related coherence-based methods for structural studies. This article specifically includes the overall object size in the analysis of the fluence and dose requirements for coherent imaging in order to investigate whether there is a dependence on object size. The applicability of the dose-fractionation theorem is also discussed. The analysis is extended to absorption-based imaging and imaging by incoherent scattering (Compton) and fluorescence. This article includes analysis of the dose required for imaging specific low-contrast cellular organelles as well as for protein against water. This article concludes that for both absorption-based and coherent diffraction imaging, the dose-fractionation theorem applies and the required dose is independent of the overall size of the object. For incoherent-imaging methods such as Compton scattering, the required dose depends on the X-ray path length through the specimen. For all three types of imaging, the dependence of fluence and dose on a resolution d goes as 1/d 4 when imaging uniform-density voxels. The independence of CDI on object size means that there is no advantage for Compton scattering over coherent-based imaging methods. The most optimistic estimate of achievable resolution is 3 nm for imaging protein molecules in water/ice using lensless imaging methods in the water window. However, the attainable resolution depends on a variety of assumptions including the model for radiation damage as a function of resolution, the efficiency of any phase-retrieval process, the actual contrast of the feature of interest within the cell and the definition of resolution itself. There is insufficient observational information available regarding the most appropriate model for radiation damage in frozen hydrated biological material. It is advocated that, in order to compare theory with experiment, standard methods of reporting results covering parameters such as the feature examined (e.g. which cellular organelle), resolution, contrast, depth of the material (for 2D), estimate of noise and dose should be adopted.
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Affiliation(s)
- Colin Nave
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
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22
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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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23
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Loetgering L, Baluktsian M, Keskinbora K, Horstmeyer R, Wilhein T, Schütz G, Eikema KSE, Witte S. Generation and characterization of focused helical x-ray beams. SCIENCE ADVANCES 2020; 6:eaax8836. [PMID: 32110725 PMCID: PMC7021491 DOI: 10.1126/sciadv.aax8836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/26/2019] [Indexed: 05/06/2023]
Abstract
The phenomenon of orbital angular momentum (OAM) affects a variety of important applications in visible optics, including optical tweezers, free-space communication, and 3D localization for fluorescence imaging. The lack of suitable wavefront shaping optics such as spatial light modulators has inhibited the ability to impart OAM on x-ray and electron radiation in a controlled way. Here, we report the experimental observation of helical soft x-ray beams generated by holographically designed diffractive optical elements. We demonstrate that these beams rotate as a function of propagation distance and measure their vorticity and coherent mode structure using ptychography. Our results establish an approach for controlling and shaping of complex focused beams for short wavelength scanning microscopy and OAM-driven applications.
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Affiliation(s)
- Lars Loetgering
- Advanced Research Center for Nanolithography, Science Park 106, 1098 XG Amsterdam, Netherlands
- Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, Netherlands
- Corresponding author. (L.L.); (S.W.)
| | - Margarita Baluktsian
- Max Planck Institute for Intelligent Systems, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | - Kahraman Keskinbora
- Max Planck Institute for Intelligent Systems, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | | | - Thomas Wilhein
- University of Applied Science Koblenz, Institute for X-Optics, Joseph-Rovan-Allee 2, 53424 Remagen, Germany
| | - Gisela Schütz
- Max Planck Institute for Intelligent Systems, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | - Kjeld S. E. Eikema
- Advanced Research Center for Nanolithography, Science Park 106, 1098 XG Amsterdam, Netherlands
- Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, Netherlands
| | - Stefan Witte
- Advanced Research Center for Nanolithography, Science Park 106, 1098 XG Amsterdam, Netherlands
- Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, Netherlands
- Corresponding author. (L.L.); (S.W.)
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24
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Odstrčil M, Holler M, Raabe J, Guizar-Sicairos M. Alignment methods for nanotomography with deep subpixel accuracy. OPTICS EXPRESS 2019; 27:36637-36652. [PMID: 31873438 DOI: 10.1364/oe.27.036637] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
As the resolution of X-ray tomography improves, the limited long-term stability and accuracy of nanoimaging tools does not allow computing artifact-free three-dimensional (3D) reconstructions without an additional step of numerical alignment of the measured projections. However, the common iterative alignment methods are significantly more computationally demanding than a simple tomographic reconstruction of the acquired volume. Here, we address this issue and present an alignment toolkit, which exploits methods with deep-subpixel accuracy combined with a multi-resolution scheme. This leads to robust and accurate alignment with significantly reduced computational and memory requirements. The performance of the presented methods is demonstrated on simulated and measured datasets for tomography and also laminography acquisition geometries. A GPU accelerated implementation of our alignment framework is publicly available.
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25
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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.
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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
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26
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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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27
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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: 26] [Impact Index Per Article: 5.2] [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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28
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Weinhardt V, Chen JH, Ekman A, McDermott G, Le Gros MA, Larabell C. Imaging cell morphology and physiology using X-rays. Biochem Soc Trans 2019; 47:489-508. [PMID: 30952801 PMCID: PMC6716605 DOI: 10.1042/bst20180036] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/02/2019] [Accepted: 01/09/2019] [Indexed: 02/07/2023]
Abstract
Morphometric measurements, such as quantifying cell shape, characterizing sub-cellular organization, and probing cell-cell interactions, are fundamental in cell biology and clinical medicine. Until quite recently, the main source of morphometric data on cells has been light- and electron-based microscope images. However, many technological advances have propelled X-ray microscopy into becoming another source of high-quality morphometric information. Here, we review the status of X-ray microscopy as a quantitative biological imaging modality. We also describe the combination of X-ray microscopy data with information from other modalities to generate polychromatic views of biological systems. For example, the amalgamation of molecular localization data, from fluorescence microscopy or spectromicroscopy, with structural information from X-ray tomography. This combination of data from the same specimen generates a more complete picture of the system than that can be obtained by a single microscopy method. Such multimodal combinations greatly enhance our understanding of biology by combining physiological and morphological data to create models that more accurately reflect the complexities of life.
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Affiliation(s)
- Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Anatomy, University of California San Francisco, San Francisco, California, U.S.A
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Axel Ekman
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Gerry McDermott
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Mark A Le Gros
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Anatomy, University of California San Francisco, San Francisco, California, U.S.A
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.
- Department of Anatomy, University of California San Francisco, San Francisco, California, U.S.A
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29
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Odstrcil M, Lebugle M, Lachat T, Raabe J, Holler M. Fast positioning for X-ray scanning microscopy by a combined motion of sample and beam-defining optics. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:504-509. [PMID: 30855261 PMCID: PMC6412177 DOI: 10.1107/s160057751801785x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/18/2018] [Indexed: 05/18/2023]
Abstract
Scanning X-ray microscopy such as X-ray ptychography requires accurate and fast positioning of samples in the X-ray beam. Sample stages often have a high mobile mass as they may carry additional mechanics or mirrors for position measurements. The high mobile mass of a piezo stage can introduce vibrations in the setup that will lead to imaging quality deterioration. Sample stages also require a large travel range which results in a slow positioning step response and thus high positioning overhead. Moving lightweight X-ray optics, such as focusing Fresnel zone plates, instead of the sample can improve the situation but it may lead to undesired variations in the illumination probe which may result in reconstruction artifacts. This paper presents a combined approach in which a slow sample stage mechanism covers the long distance range for a large field of view, and a light-weight optics scanner with a small travel range creates a superimposed motion to achieve a fast step response. The step response in the ptychographic tomography instrument used was thereby improved by an order of magnitude, allowing for efficient measurement without loss of imaging quality.
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Affiliation(s)
- Michal Odstrcil
- Swiss Light Source, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Maxime Lebugle
- Laboratory for Micro and Nanotechnology, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Thierry Lachat
- Swiss Light Source, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Jörg Raabe
- Swiss Light Source, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Mirko Holler
- Swiss Light Source, Paul Scherrer Institute, Villigen 5232, Switzerland
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30
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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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31
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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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32
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GILLES M, NASHED Y, DU M, JACOBSEN C, WILD S. 3D X-Ray Imaging of Continuous Objects beyond the Depth of Focus Limit. OPTICA 2018; 5:1078-1086. [PMID: 30406160 PMCID: PMC6217975 DOI: 10.1364/optica.5.001078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/02/2018] [Indexed: 05/08/2023]
Abstract
X-ray ptychography is becoming the standard method for sub-30 nm imaging of thick extended samples. Available algorithms and computing power have traditionally restricted sample reconstruction to 2D slices. We build on recent progress in optimization algorithms and high performance computing to solve the ptychographic phase retrieval problem directly in 3D. Our approach addresses samples that do not fit entirely within the depth of focus of the imaging system. Such samples pose additional challenges because of internal diffraction effects within the sample. We demonstrate our approach on a computational sample modeled with 17 million complex variables.
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Affiliation(s)
- M.A. GILLES
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
- Center for Applied Mathematics, Cornell University, Ithaca, New York 14853, USA
| | - Y.S.G. NASHED
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - M. DU
- Department of Materials Science & Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - C. 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
| | - S.M. WILD
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
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33
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Bernhardt M, Nicolas JD, Osterhoff M, Mittelstädt H, Reuss M, Harke B, Wittmeier A, Sprung M, Köster S, Salditt T. Correlative microscopy approach for biology using X-ray holography, X-ray scanning diffraction and STED microscopy. Nat Commun 2018; 9:3641. [PMID: 30194418 PMCID: PMC6128893 DOI: 10.1038/s41467-018-05885-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/30/2018] [Indexed: 12/31/2022] Open
Abstract
We present a correlative microscopy approach for biology based on holographic X-ray imaging, X-ray scanning diffraction, and stimulated emission depletion (STED) microscopy. All modalities are combined into the same synchrotron endstation. In this way, labeled and unlabeled structures in cells are visualized in a complementary manner. We map out the fluorescently labeled actin cytoskeleton in heart tissue cells and superimpose the data with phase maps from X-ray holography. Furthermore, an array of local far-field diffraction patterns is recorded in the regime of small-angle X-ray scattering (scanning SAXS), which can be interpreted in terms of biomolecular shape and spatial correlations of all contributing scattering constituents. We find that principal directions of anisotropic diffraction patterns coincide to a certain degree with the actin fiber directions and that actin stands out in the phase maps from holographic recordings. In situ STED recordings are proposed to formulate models for diffraction data based on co-localization constraints.
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Affiliation(s)
- M Bernhardt
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany
| | - J-D Nicolas
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany
| | - M Osterhoff
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany
| | - H Mittelstädt
- Abberior Instruments, Hans-Adolf-Krebs-Weg 1, D-37077, Göttingen, Germany
| | - M Reuss
- Abberior Instruments, Hans-Adolf-Krebs-Weg 1, D-37077, Göttingen, Germany
| | - B Harke
- Abberior Instruments, Hans-Adolf-Krebs-Weg 1, D-37077, Göttingen, Germany
| | - A Wittmeier
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany
| | - M Sprung
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 47c, D-22607, Hamburg, Germany
| | - S Köster
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany
| | - T Salditt
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany.
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34
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Victor TW, Easthon LM, Ge M, O'Toole KH, Smith RJ, Huang X, Yan H, Allen KN, Chu YS, Miller LM. X-ray Fluorescence Nanotomography of Single Bacteria with a Sub-15 nm Beam. Sci Rep 2018; 8:13415. [PMID: 30194316 PMCID: PMC6128931 DOI: 10.1038/s41598-018-31461-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 07/20/2018] [Indexed: 11/14/2022] Open
Abstract
X-ray Fluorescence (XRF) microscopy is a growing approach for imaging the trace element concentration, distribution, and speciation in biological cells at the nanoscale. Moreover, three-dimensional nanotomography provides the added advantage of imaging subcellular structure and chemical identity in three dimensions without the need for staining or sectioning of cells. To date, technical challenges in X-ray optics, sample preparation, and detection sensitivity have limited the use of XRF nanotomography in this area. Here, XRF nanotomography was used to image the elemental distribution in individual E. coli bacterial cells using a sub-15 nm beam at the Hard X-ray Nanoprobe beamline (HXN, 3-ID) at NSLS-II. These measurements were simultaneously combined with ptychography to image structural components of the cells. The cells were embedded in small (3-20 µm) sodium chloride crystals, which provided a non-aqueous matrix to retain the three-dimensional structure of the E. coli while collecting data at room temperature. Results showed a generally uniform distribution of calcium in the cells, but an inhomogeneous zinc distribution, most notably with concentrated regions of zinc at the polar ends of the cells. This work demonstrates that simultaneous two-dimensional ptychography and XRF nanotomography can be performed with a sub-15 nm beam size on unfrozen biological cells to co-localize elemental distribution and nanostructure simultaneously.
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Affiliation(s)
- Tiffany W Victor
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | | | - Mingyuan Ge
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | | | - Randy J Smith
- 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
| | - Hanfei Yan
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - Yong S Chu
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Lisa M Miller
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA.
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA.
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35
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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.
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Affiliation(s)
- Colin Nave
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Correspondence e-mail:
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36
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Pan X, Liu C, Zhu J. Coherent amplitude modulation imaging based on partially saturated diffraction pattern. OPTICS EXPRESS 2018; 26:21929-21938. [PMID: 30130894 DOI: 10.1364/oe.26.021929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/26/2018] [Indexed: 06/08/2023]
Abstract
A single-shot phase retrieval algorithm based on a random aperture and partially saturated diffraction pattern is proposed. The diffraction pattern in the saturated area could be retrieved during the iterative process, which circumvents the problem of limited dynamic range of the detector. Besides, the random aperture is easier to be manufactured and if the accuracy of the random aperture is high enough, the design value could be used directly for iterations. It has the potential to be adapted for different wavelengths without additional transmission measurement of the wave modulator. The validity has been demonstrated by simulations and experiment.
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37
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Odstrčil M, Holler M, Guizar-Sicairos M. Arbitrary-path fly-scan ptychography. OPTICS EXPRESS 2018; 26:12585-12593. [PMID: 29801297 DOI: 10.1364/oe.26.012585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
Ptychography is a coherent diffractive imaging method that can provide a diffraction-limited, robust reconstruction of the sample's complex transmission function without the use of high-quality optics. However, the scanning nature of conventional X-ray ptychography unavoidably requires the mechanical motion of either the illumination probe or the sample. In order to avoid overhead related to breaking and acceleration for every scan position, so-called fly-scan methods were developed. Here, we present an improved variant that removes the limitation of continuous scanning along a linear scanning path and allows for ptychographic reconstruction of scans taken along an arbitrary 2D continuous trajectory. We also demonstrate numerically and experimentally that our method provides significantly improved robustness against noise, particularly for larger fly-scan steps, i.e. sample shift during an exposure, which will gain importance with the advent of 4th generation synchrotron sources, where the available coherent flux may be increased by orders of magnitude. Finally, we show that the use of a spiral scan continuous trajectory alleviates significantly raster grid artifacts.
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38
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Holler M, Raabe J, Diaz A, Guizar-Sicairos M, Wepf R, Odstrcil M, Shaik FR, Panneels V, Menzel A, Sarafimov B, Maag S, Wang X, Thominet V, Walther H, Lachat T, Vitins M, Bunk O. OMNY-A tOMography Nano crYo stage. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:043706. [PMID: 29716370 DOI: 10.1063/1.5020247] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
For many scientific questions gaining three-dimensional insight into a specimen can provide valuable information. We here present an instrument called "tOMography Nano crYo (OMNY)," dedicated to high resolution 3D scanning x-ray microscopy at cryogenic conditions via hard X-ray ptychography. Ptychography is a lens-less imaging method requiring accurate sample positioning. In OMNY, this in achieved via dedicated laser interferometry and closed-loop position control reaching sub-10 nm positioning accuracy. Cryogenic sample conditions are maintained via conductive cooling. 90 K can be reached when using liquid nitrogen as coolant, and 10 K is possible with liquid helium. A cryogenic sample-change mechanism permits measurements of cryogenically fixed specimens. We compare images obtained with OMNY with older measurements performed using a nitrogen gas cryo-jet of stained, epoxy-embedded retina tissue and of frozen-hydrated Chlamydomonas cells.
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Affiliation(s)
- M Holler
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - J Raabe
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - A Diaz
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | | | - R Wepf
- Scientific Center for Optical and Electron Microscopy ScopeM, ETH Zurich, Zurich, Switzerland
| | - M Odstrcil
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - F R Shaik
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - V Panneels
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - A Menzel
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - B Sarafimov
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - S Maag
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - X Wang
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - V Thominet
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - H Walther
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - T Lachat
- EnDes Engineering Partner AG, 4703 Kestenholz, Switzerland
| | - M Vitins
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - O Bunk
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
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39
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Miao J. Multi-model imaging of the interaction of nanomaterials with cells. IUCRJ 2018; 5:122-123. [PMID: 29765600 PMCID: PMC5947715 DOI: 10.1107/s2052252518003548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A multi-model X-ray imaging approach was implemented to probe the interaction of nanomaterials with a mammalian cell in three dimensions. With further developments, this approach could have an impact on nanomedicine and nanotoxicology.
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Affiliation(s)
- Jianwei Miao
- Department of Physics and Astronomy, and California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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40
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Skjønsfjell ETB, Kleiven D, Patil N, Chushkin Y, Zontone F, Gibaud A, Breiby DW. High-resolution coherent x-ray diffraction imaging of metal-coated polymer microspheres. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2018; 35:A7-A17. [PMID: 29328079 DOI: 10.1364/josaa.35.0000a7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
Coherent x-ray diffraction imaging (CXDI) is becoming an important 3D quantitative microscopy technique, allowing structural investigation of a wide range of delicate mesoscale samples that cannot be imaged by other techniques like electron microscopy. Here we report high-resolution 3D CXDI performed on spherical microcomposites consisting of a polymer core coated with a triple layer of nickel-gold-silica. These composites are of high interest to the microelectronics industry, where they are applied in conducting adhesives as fine-pitch electrical contacts-which requires an exceptional degree of uniformity and reproducibility. Experimental techniques that can assess the state of the composites non-destructively, preferably also while embedded in electronic chips, are thus in high demand. We demonstrate that using CXDI, all four different material components of the composite could be identified, with radii matching well to the nominal specifications of the manufacturer. Moreover, CXDI provided detailed maps of layer thicknesses, roughnesses, and defects such as holes, thus also facilitating cross-layer correlations. The side length of the voxels in the reconstruction, given by the experimental geometry, was 16 nm. The effective resolution enabled resolving even the thinnest coating layer of ∼20 nm nominal width. We discuss critically the influence of the weak phase approximation and the projection approximation on the reconstructed electron density estimates, demonstrating that the latter has to be employed. We conclude that CXDI has excellent potential as a metrology tool for microscale composites.
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Du M, Jacobsen C. Relative merits and limiting factors for x-ray and electron microscopy of thick, hydrated organic materials. Ultramicroscopy 2018; 184:293-309. [PMID: 29073575 PMCID: PMC5696083 DOI: 10.1016/j.ultramic.2017.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/05/2017] [Indexed: 12/01/2022]
Abstract
Electron and x-ray microscopes allow one to image the entire, unlabeled structure of hydrated materials at a resolution well beyond what visible light microscopes can achieve. However, both approaches involve ionizing radiation, so that radiation damage must be considered as one of the limits to imaging. Drawing upon earlier work, we describe here a unified approach to estimating the image contrast (and thus the required exposure and corresponding radiation dose) in both x-ray and electron microscopy. This approach accounts for factors such as plural and inelastic scattering, and (in electron microscopy) the use of energy filters to obtain so-called "zero loss" images. As expected, it shows that electron microscopy offers lower dose for specimens thinner than about 1 µm (such as for studies of macromolecules, viruses, bacteria and archaebacteria, and thin sectioned material), while x-ray microscopy offers superior characteristics for imaging thicker specimen such as whole eukaryotic cells, thick-sectioned tissues, and organs. The required radiation dose scales strongly as a function of the desired spatial resolution, allowing one to understand the limits of live and frozen hydrated specimen imaging. Finally, we consider the factors limiting x-ray microscopy of thicker materials, suggesting that specimens as thick as a whole mouse brain can be imaged with x-ray microscopes without significant image degradation should appropriate image reconstruction methods be identified.
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Affiliation(s)
- Ming Du
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston IL 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne IL 60439, USA; Department of Physics & Astronomy, Northwestern University, 2145 Sheridan Road, Evanston IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston IL 60208, USA.
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42
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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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43
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Holler M, Raabe J, Wepf R, Shahmoradian SH, Diaz A, Sarafimov B, Lachat T, Walther H, Vitins M. OMNY PIN-A versatile sample holder for tomographic measurements at room and cryogenic temperatures. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:113701. [PMID: 29195351 DOI: 10.1063/1.4996092] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nowadays ptychographic tomography in the hard x-ray regime, i.e., at energies above about 2 keV, is a well-established measurement technique. At the Paul Scherrer Institut, currently two instruments are available: one is measuring at room temperature and atmospheric pressure, and the other, the so-called OMNY (tOMography Nano crYo) instrument, is operating at ultra-high vacuum and offering cryogenic sample temperatures down to 10 K. In this manuscript, we present the sample mounts that were developed for these instruments. Aside from excellent mechanical stability and thermal conductivity, they also offer highly reproducible mounting. Various types were developed for different kinds of samples and are presented in detail, including examples of how specimens can be mounted on these holders. We also show the first hard x-ray ptychographic tomography measurements of high-pressure frozen biological samples, in the present case Chlamydomonas cells, the related sample pins and preparation steps. For completeness, we present accessories such as transportation containers for both room temperature and cryogenic samples and a gripper mechanism for automatic sample changing. The sample mounts are not limited to x-ray tomography or hard x-ray energies, and we believe that they can be very useful for other instrumentation projects.
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Affiliation(s)
- M Holler
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - J Raabe
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - R Wepf
- Scientific Center for Optical and Electron Microscopy ScopeM, ETH Zurich, 8093 Zürich, Switzerland
| | | | - A Diaz
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - B Sarafimov
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - T Lachat
- EnDes Engineering Partner AG, 4703 Kestenholz, Switzerland
| | - H Walther
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - M Vitins
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
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Frank V, Chushkin Y, Fröhlich B, Abuillan W, Rieger H, Becker AS, Yamamoto A, Rossetti FF, Kaufmann S, Lanzer M, Zontone F, Tanaka M. Lensless Tomographic Imaging of Near Surface Structures of Frozen Hydrated Malaria-Infected Human Erythrocytes by Coherent X-Ray Diffraction Microscopy. Sci Rep 2017; 7:14081. [PMID: 29074975 PMCID: PMC5658481 DOI: 10.1038/s41598-017-14586-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 10/12/2017] [Indexed: 12/02/2022] Open
Abstract
Lensless, coherent X-ray diffraction microscopy has been drawing considerable attentions for tomographic imaging of whole human cells. In this study, we performed cryogenic coherent X-ray diffraction imaging of human erythrocytes with and without malaria infection. To shed light on structural features near the surface, “ghost cells” were prepared by the removal of cytoplasm. From two-dimensional images, we found that the surface of erythrocytes after 32 h of infection became much rougher compared to that of healthy, uninfected erythrocytes. The Gaussian roughness of an infected erythrocyte surface (69 nm) is about two times larger than that of an uninfected one (31 nm), reflecting the formation of protein knobs on infected erythrocyte surfaces. Three-dimensional tomography further enables to obtain images of the whole cells with no remarkable radiation damage, whose accuracy was estimated using phase retrieval transfer functions to be as good as 64 nm for uninfected and 80 nm for infected erythrocytes, respectively. Future improvements in phase retrieval algorithm, increase in degree of coherence, and higher flux in combination with complementary X-ray fluorescence are necessary to gain both structural and chemical details of mesoscopic architectures, such as cytoskeletons, membraneous structures, and protein complexes, in frozen hydrated human cells, especially under diseased states.
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Affiliation(s)
- Viktoria Frank
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120, Heidelberg, Germany
| | - Yuriy Chushkin
- European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France.
| | - Benjamin Fröhlich
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120, Heidelberg, Germany
| | - Wasim Abuillan
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120, Heidelberg, Germany
| | - Harden Rieger
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120, Heidelberg, Germany.,Department of Infectious Diseases, Parasitology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Alexandra S Becker
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120, Heidelberg, Germany
| | - Akihisa Yamamoto
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120, Heidelberg, Germany.,Institute for Integrated Cell-Material Sciences (WPI iCeMS), Kyoto University, 606-8501, Kyoto, Japan
| | - Fernanda F Rossetti
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120, Heidelberg, Germany.,Institute for Integrated Cell-Material Sciences (WPI iCeMS), Kyoto University, 606-8501, Kyoto, Japan
| | - Stefan Kaufmann
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120, Heidelberg, Germany
| | - Michael Lanzer
- Department of Infectious Diseases, Parasitology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Federico Zontone
- European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Motomu Tanaka
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120, Heidelberg, Germany. .,Institute for Integrated Cell-Material Sciences (WPI iCeMS), Kyoto University, 606-8501, Kyoto, Japan.
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Abstract
Water-window x-ray microscopy allows two- and three-dimensional (2D and 3D) imaging of intact unstained cells in their cryofixed near-native state with unique contrast and high resolution. Present operational biological water-window microscopes are based at synchrotron facilities, which limits their accessibility and integration with complementary methods. Laboratory-source microscopes have had difficulty addressing relevant biological tasks with proper resolution and contrast due to long exposure times and limited up-time. Here we report on laboratory cryo x-ray microscopy with the exposure time, contrast, and reliability to allow for routine high-spatial resolution 3D imaging of intact cells and cell-cell interactions. Stabilization of the laser-plasma source combined with new optics and sample preparation provide high-resolution cell imaging, both in 2D with ten-second exposures and in 3D with twenty-minute tomography. Examples include monitoring of the distribution of carbon-dense vesicles in starving HEK293T cells and imaging the interaction between natural killer cells and target cells.
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46
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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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47
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Jacobsen C, Deng J, Nashed Y. Strategies for high-throughput focused-beam ptychography. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:1078-1081. [PMID: 28862631 PMCID: PMC5580791 DOI: 10.1107/s1600577517009869] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/03/2017] [Indexed: 05/18/2023]
Abstract
X-ray ptychography is being utilized for a wide range of imaging experiments with a resolution beyond the limit of the X-ray optics used. Introducing a parameter for the ptychographic resolution gain Gp (the ratio of the beam size over the achieved pixel size in the reconstructed image), strategies for data sampling and for increasing imaging throughput when the specimen is at the focus of an X-ray beam are considered. The tradeoffs between large and small illumination spots are examined.
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Affiliation(s)
- Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, USA
- Department of Physics and Astronomy, Northwestern University, USA
- Chemistry of Life Processes Institute, Northwestern University, USA
- Correspondence e-mail:
| | - Junjing Deng
- Advanced Photon Source, Argonne National Laboratory, USA
| | - Youssef Nashed
- Mathematics and Computer Science Division, Argonne National Laboratory, USA
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