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Low-dose shift- and rotation-invariant diffraction recognition imaging. Sci Rep 2022; 12:11202. [PMID: 35778504 PMCID: PMC9249920 DOI: 10.1038/s41598-022-15486-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/24/2022] [Indexed: 12/04/2022] Open
Abstract
A low-dose imaging technique which uses recognition rather than recording of a full high-resolution image is proposed. A structural hypothesis is verified by probing the object with only a few particles (photons, electrons). Each scattered particle is detected in the far field and its position on the detector is analysed by applying Bayesian statistics. Already a few detected particles are sufficient to confirm a structural hypothesis at a probability exceeding 95%. As an example, the method is demonstrated as an application in optical character recognition, where a hand-written number is recognized from a set of different written numbers. In other provided examples, the structural hypothesis of a single macromolecule is recognized from a diffraction pattern acquired at an extremely low radiation dose, less than one X-ray photon or electron per Å2, thus leaving the macromolecule practically without any radiation damage. The proposed principle of low-dose recognition can be utilized in various applications, ranging from optical character recognition and optical security elements to recognizing a certain protein or its conformation.
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2
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Latychevskaia T. Holography and Coherent Diffraction Imaging with Low-(30-250 eV) and High-(80-300 keV) Energy Electrons: History, Principles, and Recent Trends. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E3089. [PMID: 32664297 PMCID: PMC7412140 DOI: 10.3390/ma13143089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 01/02/2023]
Abstract
In this paper, we present the theoretical background to electron scattering in an atomic potential and the differences between low- and high-energy electrons interacting with matter. We discuss several interferometric techniques that can be realized with low- and high-energy electrons and which can be applied to the imaging of non-crystalline samples and individual macromolecules, including in-line holography, point projection microscopy, off-axis holography, and coherent diffraction imaging. The advantages of using low- and high-energy electrons for particular experiments are examined, and experimental schemes for holography and coherent diffraction imaging are compared.
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Affiliation(s)
- Tatiana Latychevskaia
- Physics Institute, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland;
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
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3
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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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4
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Latychevskaia T, Fink HW. Three-dimensional double helical DNA structure directly revealed from its X-ray fiber diffraction pattern by iterative phase retrieval. OPTICS EXPRESS 2018; 26:30991-31017. [PMID: 30469988 DOI: 10.1364/oe.26.030991] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/24/2018] [Indexed: 06/09/2023]
Abstract
Coherent diffraction imaging (CDI) allows the retrieval of an isolated object's structure, such as a macromolecule, from its diffraction pattern. CDI requires the fulfillment of two conditions: the imaging radiation must be coherent and the object must be isolated. We discuss that it is possible to directly retrieve the molecular structure from its diffraction pattern, which was acquired neither with coherent radiation nor from an individual molecule. This is provided that the molecule exhibits periodicity in one direction, as in the case of fiber diffraction. We demonstrate that, when we apply iterative phase retrieval methods to a fiber diffraction pattern, the repeating unit; that is, the molecule structure, can directly be reconstructed without any prior modeling. For example, we recover the the DNA double helix's structure in three-dimensions from its two-dimensional X-ray fiber diffraction pattern, Photograph (Photo) 51, which was acquired in Raymond Gosling and Rosalind Franklin's famous experiment at a resolution of 3.4 Å.
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5
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Current Status of Single Particle Imaging with X-ray Lasers. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8010132] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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6
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Jones MW, Dearnley MK, van Riessen GA, Abbey B, Putkunz CT, Junker MD, Vine DJ, McNulty I, Nugent KA, Peele AG, Tilley L. Rapid, low dose X-ray diffractive imaging of the malaria parasite Plasmodium falciparum. Ultramicroscopy 2014; 143:88-92. [DOI: 10.1016/j.ultramic.2013.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 09/23/2013] [Accepted: 09/23/2013] [Indexed: 11/30/2022]
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7
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Jones MWM, van Riessen GA, Abbey B, Putkunz CT, Junker MD, Balaur E, Vine DJ, McNulty I, Chen B, Arhatari BD, Frankland S, Nugent KA, Tilley L, Peele AG. Whole-cell phase contrast imaging at the nanoscale using Fresnel coherent diffractive imaging tomography. Sci Rep 2014; 3:2288. [PMID: 23887204 PMCID: PMC3724183 DOI: 10.1038/srep02288] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 07/10/2013] [Indexed: 11/29/2022] Open
Abstract
X-ray tomography can provide structural information of whole cells in close to their native state. Radiation-induced damage, however, imposes a practical limit to image resolution, and as such, a choice between damage, image contrast, and image resolution must be made. New coherent diffractive imaging techniques, such Fresnel Coherent Diffractive Imaging (FCDI), allows quantitative phase information with exceptional dose efficiency, high contrast, and nano-scale resolution. Here we present three-dimensional quantitative images of a whole eukaryotic cell by FCDI at a spatial resolution below 70 nm with sufficient phase contrast to distinguish major cellular components. From our data, we estimate that the minimum dose required for a similar resolution is close to that predicted by the Rose criterion, considerably below accepted estimates of the maximum dose a frozen-hydrated cell can tolerate. Based on the dose efficiency, contrast, and resolution achieved, we expect this technique will find immediate applications in tomographic cellular characterisation.
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Affiliation(s)
- Michael W M Jones
- ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086, Australia
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8
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Jones MWM, Abbey B, Gianoncelli A, Balaur E, Millet C, Luu MB, Coughlan HD, Carroll AJ, Peele AG, Tilley L, van Riessen GA. Phase-diverse Fresnel coherent diffractive imaging of malaria parasite-infected red blood cells in the water window. OPTICS EXPRESS 2013; 21:32151-32159. [PMID: 24514809 DOI: 10.1364/oe.21.032151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Phase-diverse Fresnel coherent diffractive imaging has been shown to reveal the structure and composition of biological specimens with high sensitivity at nanoscale resolution. However, the method has yet to be applied using X-ray illumination with energy in the so-called 'water-window' that lies between the carbon and oxygen K edges. In this range, differences in the strength of the X-ray interaction for protein based biological materials and water is increased. Here we demonstrate a proof-of-principle application of FCDI at an X-ray energy within the water-window to a dehydrated cellular sample composed of red blood cells infected with the trophozoite stage of the malaria parasite, Plasmodium falciparum. Comparison of the results to both optical and electron microscopy shows that the correlative imaging methods that include water-window FCDI will find utility in studying cellular architecture.
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Jones MWM, Peele AG, van Riessen GA. Application of a complex constraint for biological samples in coherent diffractive imaging. OPTICS EXPRESS 2013; 21:30275-30281. [PMID: 24514606 DOI: 10.1364/oe.21.030275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We demonstrate the application of a complex constraint in the reconstruction of images from phase-diverse Fresnel coherent diffraction data for heterogeneous biological objects. The application of this constraint is shown to improve the quality of the reconstruction of both the phase and the magnitude of the complex object transmission function.
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11
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Flewett S, Günther CM, Schmising CVK, Pfau B, Mohanty J, Büttner F, Riemeier M, Hantschmann M, Kläui M, Eisebitt S. Holographically aided iterative phase retrieval. OPTICS EXPRESS 2012; 20:29210-6. [PMID: 23388746 DOI: 10.1364/oe.20.029210] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Fourier transform holography (FTH) is a noise-resistant imaging technique which allows for nanometer spatial resolution x-ray imaging, where the inclusion of a small reference scattering object provides the otherwise missing phase information. With FTH, one normally requires a considerable distance between the sample and the reference to ensure spatial separation of the reconstruction and its autocorrelation. We demonstrate however that this requirement can be omitted at the small cost of iteratively separating the reconstruction and autocorrelation. In doing so, the photon efficiency of FTH can be increased due to a smaller illumination area, and we show how the presence of the reference prevents the non-uniqueness problems often encountered with plane-wave iterative phase retrieval. The method was tested on a cobalt/platinum multilayer exhibiting out of plane magnetized domains, where the magnetic circular dichroism effect was used to image the magnetic domains at the cobalt L₃-edge at 780eV.
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Affiliation(s)
- S Flewett
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin,Germany.
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12
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Latychevskaia T, Longchamp JN, Fink HW. When holography meets coherent diffraction imaging. OPTICS EXPRESS 2012; 20:28871-28892. [PMID: 23263128 DOI: 10.1364/oe.20.028871] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The phase problem is inherent to crystallographic, astronomical and optical imaging where only the intensity of the scattered signal is detected and the phase information is lost and must somehow be recovered to reconstruct the object's structure. Modern imaging techniques at the molecular scale rely on utilizing novel coherent light sources like X-ray free electron lasers for the ultimate goal of visualizing such objects as individual biomolecules rather than crystals. Here, unlike in the case of crystals where structures can be solved by model building and phase refinement, the phase distribution of the wave scattered by an individual molecule must directly be recovered. There are two well-known solutions to the phase problem: holography and coherent diffraction imaging (CDI). Both techniques have their pros and cons. In holography, the reconstruction of the scattered complex-valued object wave is directly provided by a well-defined reference wave that must cover the entire detector area which often is an experimental challenge. CDI provides the highest possible, only wavelength limited, resolution, but the phase recovery is an iterative process which requires some pre-defined information about the object and whose outcome is not always uniquely-defined. Moreover, the diffraction patterns must be recorded under oversampling conditions, a pre-requisite to be able to solve the phase problem. Here, we report how holography and CDI can be merged into one superior technique: holographic coherent diffraction imaging (HCDI). An inline hologram can be recorded by employing a modified CDI experimental scheme. We demonstrate that the amplitude of the Fourier transform of an inline hologram is related to the complex-valued visibility, thus providing information on both, the amplitude and the phase of the scattered wave in the plane of the diffraction pattern. With the phase information available, the condition of oversampling the diffraction patterns can be relaxed, and the phase problem can be solved in a fast and unambiguous manner. We demonstrate the reconstruction of various diffraction patterns of objects recorded with visible light as well as with low-energy electrons. Although we have demonstrated our HCDI method using laser light and low-energy electrons, it can also be applied to any other coherent radiation such as X-rays or high-energy electrons.
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Affiliation(s)
- Tatiana Latychevskaia
- Institute of Physics, University of Zurich, Winterthurerstrasse 190, CH-8057, Switzerland.
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13
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Determination of protein subcellular localization in apicomplexan parasites. Trends Parasitol 2012; 28:546-54. [PMID: 22995720 DOI: 10.1016/j.pt.2012.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 08/22/2012] [Accepted: 08/24/2012] [Indexed: 11/20/2022]
Abstract
Parasites from the phylum Apicomplexa include causative agents of serious diseases including malaria (Plasmodium spp.) and toxoplasmosis (Toxoplasma gondii). Apicomplexan parasites infect thousands of types of animal cells and send their proteins to an array of compartments within their own cell, as well as exporting proteins into and beyond their host cell. Ascertaining destinations to which individual proteins are delivered allows researchers to better understand parasite biology and to identify potential targets for therapeutic interventions. Our toolkit for establishing subcellular locations of apicomplexan proteins is becoming more extensive and specialized, and here we review developments in this technology.
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15
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Putkunz CT, Clark JN, Vine DJ, Williams GJ, Balaur E, Cadenazzi GA, Curwood EK, Henderson CA, Scholten RE, Stewart RJ, McNulty I, Nugent KA, Peele AG. Mapping granular structure in the biological adhesive of Phragmatopoma californica using phase diverse coherent diffractive imaging. Ultramicroscopy 2011; 111:1184-8. [DOI: 10.1016/j.ultramic.2011.03.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/28/2011] [Accepted: 03/31/2011] [Indexed: 10/18/2022]
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16
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Huang X, Miao H, Nelson J, Turner J, Steinbrener J, Shapiro D, Kirz J, Jacobsen C. Anti-contamination device for cryogenic soft X-ray diffraction microscopy. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH. SECTION A, ACCELERATORS, SPECTROMETERS, DETECTORS AND ASSOCIATED EQUIPMENT 2011; 638:171-175. [PMID: 21547016 PMCID: PMC3085496 DOI: 10.1016/j.nima.2011.02.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Cryogenic microscopy allows one to view frozen hydrated biological and soft matter specimens with good structural preservation and a high degree of stability against radiation damage. We describe a liquid nitrogen-cooled anti-contamination device for cryogenic X-ray diffraction microscopy. The anti-contaminator greatly reduces the buildup of ice layers on the specimen due to condensation of residual water vapor in the experimental vacuum chamber. We show by coherent X-ray diffraction measurements that this leads to fivefold reduction of background scattering, which is important for far-field X-ray diffraction microscopy of biological specimens.
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Affiliation(s)
- Xiaojing Huang
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800, USA
- Corresponding author. Current address: London Centre for Nanotechnology, University College, London WC1H 0AH, UK. Tel.: +44 630 252 0893. , (X. Huang)
| | - Huijie Miao
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800, USA
| | - Johanna Nelson
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800, USA
| | - Joshua Turner
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800, USA
| | - Jan Steinbrener
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800, USA
| | - David Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Janos Kirz
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chris Jacobsen
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
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17
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Pelliccia D, Nikulin AY, Moser HO, Nugent KA. Experimental characterization of the coherence properties of hard x-ray sources. OPTICS EXPRESS 2011; 19:8073-8. [PMID: 21643056 DOI: 10.1364/oe.19.008073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The experimental characterization of the coherence properties of hard X-ray sources is reported and discussed. The source is described by its Mutual Optical Intensity (MOI). The coherent-mode decomposition is applied to the MOI described by a Gaussian-Schell model. The method allows for a direct, quantitative characterization of the degree of coherence of both synchrotron and laboratory sources. The latter represents the first example of characterizing a low coherence hard x-ray source.
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Affiliation(s)
- Daniele Pelliccia
- ARC Centre of Excellence for Coherent X-ray Science, School of Physics, Monash University, Victoria, Australia.
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18
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Larabell CA, Nugent KA. Imaging cellular architecture with X-rays. Curr Opin Struct Biol 2010; 20:623-31. [PMID: 20869868 PMCID: PMC3268817 DOI: 10.1016/j.sbi.2010.08.008] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 08/10/2010] [Accepted: 08/26/2010] [Indexed: 01/26/2023]
Abstract
X-ray imaging of biological samples is progressing rapidly. In this paper we review the progress to date in high-resolution imaging of cellular architecture. In particular we survey the progress in soft X-ray tomography and argue that the field is coming of age and that important biological insights are starting to emerge. We then review the new ideas based on coherent diffraction. These methods are at a much earlier stage of development but, as they eliminate the need for X-ray optics, have the capacity to provide substantially better spatial resolution than zone plate-based methods.
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Affiliation(s)
- Carolyn A Larabell
- Department of Anatomy, University of California at San Francisco, 1550 4th Street, San Francisco, CA 94158, USA.
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19
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Hanssen E, Knoechel C, Klonis N, Abu-Bakar N, Deed S, LeGros M, Larabell C, Tilley L. Cryo transmission X-ray imaging of the malaria parasite, P. falciparum. J Struct Biol 2010; 173:161-8. [PMID: 20826218 DOI: 10.1016/j.jsb.2010.08.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 08/13/2010] [Accepted: 08/25/2010] [Indexed: 11/19/2022]
Abstract
Cryo transmission X-ray microscopy in the "water window" of photon energies has recently been introduced as a method that exploits the natural contrast of biological samples. We have used cryo tomographic X-ray imaging of the intra-erythrocytic malaria parasite, Plasmodium falciparum, to undertake a survey of the cellular features of this important human pathogen. We examined whole hydrated cells at different stages of growth and defined some of the structures with different X-ray density, including the parasite nucleus, cytoplasm, digestive vacuole and the hemoglobin degradation product, hemozoin. As the parasite develops from an early cup-shaped morphology to a more rounded shape, puncta of hemozoin are formed; these coalesce in the mature trophozoite into a central compartment. In some trophozoite stage parasites we observed invaginations of the parasite surface and, using a selective permeabilization process, showed that these remain connected to the RBC cytoplasm. Some of these invaginations have large openings consistent with phagocytic structures and we observed independent endocytic vesicles in the parasite cytoplasm which appear to play a role in hemoglobin uptake. In schizont stage parasites staggered mitosis was observed and X-ray-dense lipid-rich structures were evident at their apical ends of the developing daughter cells. Treatment of parasites with the antimalarial drug artemisinin appears to affect parasite development and their ability to produce the hemoglobin breakdown product, hemozoin.
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Affiliation(s)
- Eric Hanssen
- Electron Microscopy Unit Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia.
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20
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Putkunz CT, Pfeifer MA, Peele AG, Williams GJ, Quiney HM, Abbey B, Nugent KA, McNulty I. Fresnel coherent diffraction tomography. OPTICS EXPRESS 2010; 18:11746-53. [PMID: 20589035 DOI: 10.1364/oe.18.011746] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Tomographic coherent imaging requires the reconstruction of a series of two-dimensional projections of the object. We show that using the solution for the image of one projection as the starting point for the reconstruction of the next projection offers a reliable and rapid approach to the image reconstruction. The method is demonstrated on simulated and experimental data. This technique also simplifies reconstructions using data with curved incident wavefronts.
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Affiliation(s)
- C T Putkunz
- Department of Physics, La Trobe University, Australia
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21
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High-resolution x-ray diffraction microscopy of specifically labeled yeast cells. Proc Natl Acad Sci U S A 2010; 107:7235-9. [PMID: 20368463 DOI: 10.1073/pnas.0910874107] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
X-ray diffraction microscopy complements other x-ray microscopy methods by being free of lens-imposed radiation dose and resolution limits, and it allows for high-resolution imaging of biological specimens too thick to be viewed by electron microscopy. We report here the highest resolution (11-13 nm) x-ray diffraction micrograph of biological specimens, and a demonstration of molecular-specific gold labeling at different depths within cells via through-focus propagation of the reconstructed wavefield. The lectin concanavalin A conjugated to colloidal gold particles was used to label the alpha-mannan sugar in the cell wall of the yeast Saccharomyces cerevisiae. Cells were plunge-frozen in liquid ethane and freeze-dried, after which they were imaged whole using x-ray diffraction microscopy at 750 eV photon energy.
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Clark JN, Putkunz CT, Pfeifer MA, Peele AG, Williams GJ, Chen B, Nugent KA, Hall C, Fullagar W, Kim S, McNulty I. Use of a complex constraint in coherent diffractive imaging. OPTICS EXPRESS 2010; 18:1981-1993. [PMID: 20174028 DOI: 10.1364/oe.18.001981] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We demonstrate use of a complex constraint based on the interaction of x-rays with matter for reconstructing images from coherent X-ray diffraction. We show the complementary information provided by the phase and magnitude of the reconstructed wavefield greatly improves the quality of the resulting estimate of the transmission function of an object without the need for a priori information about the object composition.
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Affiliation(s)
- J N Clark
- Department of Physics, La Trobe University, Australia
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23
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Quantitative biological imaging by ptychographic x-ray diffraction microscopy. Proc Natl Acad Sci U S A 2009; 107:529-34. [PMID: 20018650 DOI: 10.1073/pnas.0905846107] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent advances in coherent x-ray diffractive imaging have paved the way to reliable and quantitative imaging of noncompact specimens at the nanometer scale. Introduced a year ago, an advanced implementation of ptychographic coherent diffractive imaging has removed much of the previous limitations regarding sample preparation and illumination conditions. Here, we apply this recent approach toward structure determination at the nanoscale to biological microscopy. We show that the projected electron density of unstained and unsliced freeze-dried cells of the bacterium Deinococcus radiodurans can be derived from the reconstructed phase in a straightforward and reproducible way, with quantified and small errors. Thus, the approach may contribute in the future to the understanding of the highly disputed nucleoid structure of bacterial cells. In the present study, the estimated resolution for the cells was 85 nm (half-period length), whereas 50-nm resolution was demonstrated for lithographic test structures. With respect to the diameter of the pinhole used to illuminate the samples, a superresolution of about 15 was achieved for the cells and 30 for the test structures, respectively. These values should be assessed in view of the low dose applied on the order of approximately 1.3x10(5) Gy, and were shown to scale with photon fluence.
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24
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Whitehead LW, Williams GJ, Quiney HM, Vine DJ, Dilanian RA, Flewett S, Nugent KA, Peele AG, Balaur E, McNulty I. Diffractive imaging using partially coherent x rays. PHYSICAL REVIEW LETTERS 2009; 103:243902. [PMID: 20366201 DOI: 10.1103/physrevlett.103.243902] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 11/18/2009] [Indexed: 05/21/2023]
Abstract
The measured spatial coherence characteristics of the illumination used in a diffractive imaging experiment are incorporated in an algorithm that reconstructs the complex transmission function of an object from experimental x-ray diffraction data using 1.4 keV x rays. Conventional coherent diffractive imaging, which assumes full spatial coherence, is a limiting case of our approach. Even in cases in which the deviation from full spatial coherence is small, we demonstrate a significant improvement in the quality of wave field reconstructions. Our formulation is applicable to x-ray and electron diffraction imaging techniques provided that the spatial coherence properties of the illumination are known or can be measured.
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Affiliation(s)
- L W Whitehead
- School of Physics, The University of Melbourne, Victoria 3010, Australia
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Huang X, Nelson J, Kirz J, Lima E, Marchesini S, Miao H, Neiman AM, Shapiro D, Steinbrener J, Stewart A, Turner JJ, Jacobsen C. Soft X-ray diffraction microscopy of a frozen hydrated yeast cell. PHYSICAL REVIEW LETTERS 2009; 103:198101. [PMID: 20365955 PMCID: PMC2866741 DOI: 10.1103/physrevlett.103.198101] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 07/29/2009] [Indexed: 05/07/2023]
Abstract
We report the first image of an intact, frozen hydrated eukaryotic cell using x-ray diffraction microscopy, or coherent x-ray diffraction imaging. By plunge freezing the specimen in liquid ethane and maintaining it below -170 degrees C, artifacts due to dehydration, ice crystallization, and radiation damage are greatly reduced. In this example, coherent diffraction data using 520 eV x rays were recorded and reconstructed to reveal a budding yeast cell at a resolution better than 25 nm. This demonstration represents an important step towards high resolution imaging of cells in their natural, hydrated state, without limitations imposed by x-ray optics.
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Affiliation(s)
- Xiaojing Huang
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Johanna Nelson
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Janos Kirz
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Enju Lima
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Stefano Marchesini
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Huijie Miao
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Aaron M. Neiman
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA
| | - David Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Steinbrener
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Andrew Stewart
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Joshua J. Turner
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Chris Jacobsen
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
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Affiliation(s)
- Reagan McRae
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332
| | - Pritha Bagchi
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332
| | - S. Sumalekshmy
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332
| | - Christoph J. Fahrni
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332
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Flewett S, Quiney HM, Tran CQ, Nugent KA. Extracting coherent modes from partially coherent wavefields. OPTICS LETTERS 2009; 34:2198-2200. [PMID: 19823547 DOI: 10.1364/ol.34.002198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A method for numerically recovering the coherent modes and their occupancies from a known mutual optical intensity function is described. As an example, the technique is applied to previously published experimental data from an x-ray undulator source. The data are found to be described by three coherent modes, and the functional forms and relative occupancies of these modes are recovered.
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Affiliation(s)
- Samuel Flewett
- ARC Centre of Excellence for Coherent X-Ray Science, School of Physics, University of Melbourne, Victoria, Australia
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Studer D, Humbel BM, Chiquet M. Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution. Histochem Cell Biol 2008; 130:877-89. [PMID: 18795316 DOI: 10.1007/s00418-008-0500-1] [Citation(s) in RCA: 182] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2008] [Indexed: 12/17/2022]
Abstract
Transmission electron microscopy has provided most of what is known about the ultrastructural organization of tissues, cells, and organelles. Due to tremendous advances in crystallography and magnetic resonance imaging, almost any protein can now be modeled at atomic resolution. To fully understand the workings of biological "nanomachines" it is necessary to obtain images of intact macromolecular assemblies in situ. Although the resolution power of electron microscopes is on the atomic scale, in biological samples artifacts introduced by aldehyde fixation, dehydration and staining, but also section thickness reduces it to some nanometers. Cryofixation by high pressure freezing circumvents many of the artifacts since it allows vitrifying biological samples of about 200 mum in thickness and immobilizes complex macromolecular assemblies in their native state in situ. To exploit the perfect structural preservation of frozen hydrated sections, sophisticated instruments are needed, e.g., high voltage electron microscopes equipped with precise goniometers that work at low temperature and digital cameras of high sensitivity and pixel number. With them, it is possible to generate high resolution tomograms, i.e., 3D views of subcellular structures. This review describes theory and applications of the high pressure cryofixation methodology and compares its results with those of conventional procedures. Moreover, recent findings will be discussed showing that molecular models of proteins can be fitted into depicted organellar ultrastructure of images of frozen hydrated sections. High pressure freezing of tissue is the base which may lead to precise models of macromolecular assemblies in situ, and thus to a better understanding of the function of complex cellular structures.
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Affiliation(s)
- Daniel Studer
- Institute for Anatomy, University of Bern, Baltzerstr. 2, 3000, Bern 9, Switzerland.
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