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Ekman A, Weinhardt V, Chen JH, McDermott G, Le Gros MA, Larabell C. PSF correction in soft X-ray tomography. J Struct Biol 2018; 204:9-18. [PMID: 29908247 DOI: 10.1016/j.jsb.2018.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/05/2018] [Accepted: 06/07/2018] [Indexed: 11/29/2022]
Abstract
In this article, we introduce a linear approximation of the forward model of soft X-ray tomography, such that the reconstruction is solvable by standard iterative schemes. This linear model takes into account the three-dimensional point spread function (PSF) of the optical system, which consequently enhances the reconstruction of data. The feasibility of the model is demonstrated on both simulated and experimental data, based on theoretically estimated and experimentally measured PSFs.
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Affiliation(s)
- Axel Ekman
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Venera Weinhardt
- Department of Anatomy, University of California, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian-Hua Chen
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Gerry McDermott
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Mark A Le Gros
- Department of Anatomy, University of California, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Sorrentino A, Nicolás J, Valcárcel R, Chichón FJ, Rosanes M, Avila J, Tkachuk A, Irwin J, Ferrer S, Pereiro E. MISTRAL: a transmission soft X-ray microscopy beamline for cryo nano-tomography of biological samples and magnetic domains imaging. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:1112-7. [PMID: 26134819 DOI: 10.1107/s1600577515008632] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/03/2015] [Indexed: 05/12/2023]
Abstract
The performance of MISTRAL is reported, the soft X-ray transmission microscopy beamline at the ALBA light source (Barcelona, Spain) which is primarily dedicated to cryo soft X-ray tomography (cryo-SXT) for three-dimensional visualization of whole unstained cells at spatial resolutions down to 30 nm (half pitch). Short acquisition times allowing for high-throughput and correlative microscopy studies have promoted cryo-SXT as an emerging cellular imaging tool for structural cell biologists bridging the gap between optical and electron microscopy. In addition, the beamline offers the possibility of imaging magnetic domains in thin magnetic films that are illustrated here with an example.
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Affiliation(s)
- Andrea Sorrentino
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, Barcelona 08290, Spain
| | - Josep Nicolás
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, Barcelona 08290, Spain
| | - Ricardo Valcárcel
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, Barcelona 08290, Spain
| | | | - Marc Rosanes
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, Barcelona 08290, Spain
| | - Jose Avila
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, Barcelona 08290, Spain
| | | | | | - Salvador Ferrer
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, Barcelona 08290, Spain
| | - Eva Pereiro
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, Barcelona 08290, Spain
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3
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Selin M, Fogelqvist E, Holmberg A, Guttmann P, Vogt U, Hertz HM. 3D simulation of the image formation in soft x-ray microscopes. OPTICS EXPRESS 2014; 22:30756-30768. [PMID: 25607024 DOI: 10.1364/oe.22.030756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In water-window soft x-ray microscopy the studied object is typically larger than the depth of focus and the sample illumination is often partially coherent. This blurs out-of-focus features and may introduce considerable fringing. Understanding the influence of these phenomena on the image formation is therefore important when interpreting experimental data. Here we present a wave-propagation model operating in 3D for simulating the image formation of thick objects in partially coherent soft x-ray microscopes. The model is compared with present simulation methods as well as with experiments. The results show that our model predicts the image formation of transmission soft x-ray microscopes more accurately than previous models.
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Dent KC, Hagen C, Grünewald K. Critical step-by-step approaches toward correlative fluorescence/soft X-ray cryo-microscopy of adherent mammalian cells. Methods Cell Biol 2014; 124:179-216. [PMID: 25287842 DOI: 10.1016/b978-0-12-801075-4.00009-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Soft X-ray cryo-microscopy/tomography with its extraordinary capability to map vitreous cells with high absorption contrast in their full three-dimensional extent, and at a resolution exceeding super-resolution fluorescence microscopy, is a valuable tool for integrative structural cell biology. Focusing on cell biological applications, its ongoing methodological development gained momentum by combining it with fluorescence cryo-microscopy, thus correlating highly resolved structural and specific information in situ. In this chapter, we provide a basic description of the techniques, as well as an overview of equipment and methods available to carry out correlative soft X-ray cryo-tomography experiments on frozen-hydrated cells grown on a planar support. Our aim here is to suggest ways that biologically representative data can be recorded to the highest possible resolution, while also keeping in mind the limitations of the technique during data acquisition and analysis. We have written from our perspective as electron cryo-microscopists/structural cell biologists who have experience using correlative fluorescence/cryoXM/T at synchrotron beamlines presently available for external users in Europe (HZB TXM at U41-FSGM, BESSY II, Berlin/Germany; Carl Zeiss TXMs at MISTRAL, ALBA, Barcelona/Spain, and B24, DLS, Oxfordshire, UK).
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Affiliation(s)
- Kyle C Dent
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom; Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Christoph Hagen
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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Rehbein S, Guttmann P, Werner S, Schneider G. Characterization of the resolving power and contrast transfer function of a transmission X-ray microscope with partially coherent illumination. OPTICS EXPRESS 2012; 20:5830-9. [PMID: 22418460 DOI: 10.1364/oe.20.005830] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The achievable spatial resolution and the contrast transfer function (CTF) are key parameters characterizing an X-ray microscope. We measured the spatial resolution and the contrast transfer function of the transmission X-ray microscope (TXM) at the electron storage ring BESSY II. The TXM uses the radiation of an undulator source and operates under partially coherent illumination conditions. For spatial resolutions down to 25 nm, our measurements of the CTF's are in good agreement with theoretical CTF data for partial coherence. With higher resolution zone plate objectives, we measured a spatial resolution (half-pitch) of 11 nm in 1st and 3rd order of diffraction. However, with these objectives the stray light level increases significantly.
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Affiliation(s)
- Stefan Rehbein
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute for Soft Matter and Functional Materials, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
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Oton J, Sorzano COS, Pereiro E, Cuenca-Alba J, Navarro R, Carazo JM, Marabini R. Image formation in cellular X-ray microscopy. J Struct Biol 2012; 178:29-37. [PMID: 22343468 DOI: 10.1016/j.jsb.2012.01.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 01/04/2012] [Accepted: 01/05/2012] [Indexed: 01/15/2023]
Abstract
Soft X-ray Tomographic (TomoX) microscopy has become a reality in the last years. The resolution range of this technique nicely fits between confocal and electron microscopies and will play a key role in the elucidation of the organization between the molecular and the organelle levels. In fact, it offers the possibility of imaging three-dimensional structures of hydrated biological specimens near their native state without chemical pre-treatment. Ideally, TomoX reconstructs the specimen absorption coefficients from projections of this specimen, but, unfortunately, X-ray micrographs are only an approximation to projections of the specimen, resulting in inaccuracies if a tomographic reconstruction is performed without explicitly incorporating these approximations. In an attempt to mitigate some of these inaccuracies, we develop in this work an image formation model within the approximation of assuming incoherent illumination.
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Affiliation(s)
- Joaquin Oton
- Centro Nacional de Biotecnología, Ciudad Universitaria de Cantoblanco, Calle Darwin, 3, 28049 Madrid, Spain
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Schneider G, Guttmann P, Rehbein S, Werner S, Follath R. Cryo X-ray microscope with flat sample geometry for correlative fluorescence and nanoscale tomographic imaging. J Struct Biol 2012; 177:212-23. [DOI: 10.1016/j.jsb.2011.12.023] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 12/20/2011] [Accepted: 12/20/2011] [Indexed: 11/26/2022]
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McDermott G, Fox DM, Epperly L, Wetzler M, Barron AE, Le Gros MA, Larabell CA. Visualizing and quantifying cell phenotype using soft X-ray tomography. Bioessays 2012; 34:320-7. [PMID: 22290620 DOI: 10.1002/bies.201100125] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Soft X-ray tomography (SXT) is an imaging technique capable of characterizing and quantifying the structural phenotype of cells. In particular, SXT is used to visualize the internal architecture of fully hydrated, intact eukaryotic and prokaryotic cells at high spatial resolution (50 nm or better). Image contrast in SXT is derived from the biochemical composition of the cell, and obtained without the need to use potentially damaging contrast-enhancing agents, such as heavy metals. The cells are simply cryopreserved prior to imaging, and are therefore imaged in a near-native state. As a complement to structural imaging by SXT, the same specimen can now be imaged by correlated cryo-light microscopy. By combining data from these two modalities specific molecules can be localized directly within the framework of a high-resolution, three-dimensional reconstruction of the cell. This combination of data types allows sophisticated analyses to be carried out on the impact of environmental and/or genetic factors on cell phenotypes.
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Affiliation(s)
- Gerry McDermott
- Department of Anatomy, University of California, San Francisco, CA, USA
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9
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Hagen C, Guttmann P, Klupp B, Werner S, Rehbein S, Mettenleiter TC, Schneider G, Grünewald K. Correlative VIS-fluorescence and soft X-ray cryo-microscopy/tomography of adherent cells. J Struct Biol 2011; 177:193-201. [PMID: 22210307 PMCID: PMC3343273 DOI: 10.1016/j.jsb.2011.12.012] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 12/12/2011] [Accepted: 12/14/2011] [Indexed: 01/12/2023]
Abstract
Soft X-ray cryo-microscopy/tomography of vitreous samples is becoming a valuable tool in structural cell biology. Within the ‘water-window’ wavelength region (2.34–4.37 nm), it provides absorption contrast images with high signal to noise ratio and resolution of a few tens of nanometer. Soft X-rays with wavelengths close to the K-absorption edge of oxygen penetrate biological samples with thicknesses in the micrometer range. Here, we report on the application of a recently established extension of the transmission soft X-ray cryo-microscope (HZB TXM) at the beamline U41-XM of the BESSY II electron storage ring by an in-column epi-fluorescence and reflected light cryo-microscope. We demonstrate the new capability for correlative fluorescence and soft X-ray cryo-microscopy/tomography of this instrument along a typical life science experimental approach – the correlation of a fluorophore-tagged protein (pUL34-GFP of pseudorabies virus, PrV, the nuclear membrane-anchored component of the nuclear egress complex of the Herpesviridae which interacts with viral pUL31) in PrV pUL34-GFP/pUL31 coexpressing mammalian cells, with virus-induced vesicular structures in the nucleus, expanding the nucleoplasmic reticulum. Taken together, our results demonstrate new possibilities to study the role of specific proteins in substructures of adherent cells, especially of the nucleus in toto, accessible to electron microscopy in thinned samples only.
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Affiliation(s)
- Christoph Hagen
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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Hertz HM, von Hofsten O, Bertilson M, Vogt U, Holmberg A, Reinspach J, Martz D, Selin M, Christakou AE, Jerlström-Hultqvist J, Svärd S. Laboratory cryo soft X-ray microscopy. J Struct Biol 2011; 177:267-72. [PMID: 22119891 DOI: 10.1016/j.jsb.2011.11.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 11/01/2011] [Accepted: 11/09/2011] [Indexed: 11/17/2022]
Abstract
Lens-based water-window X-ray microscopy allows two- and three-dimensional (2D and 3D) imaging of intact unstained cells in their near-native state with unprecedented contrast and resolution. Cryofixation is essential to avoid radiation damage to the sample. Present cryo X-ray microscopes rely on synchrotron radiation sources, thereby limiting the accessibility for a wider community of biologists. In the present paper we demonstrate water-window cryo X-ray microscopy with a laboratory-source-based arrangement. The microscope relies on a λ=2.48-nm liquid-jet high-brightness laser-plasma source, normal-incidence multilayer condenser optics, 30-nm zone-plate optics, and a cryo sample chamber. We demonstrate 2D imaging of test patterns, and intact unstained yeast, protozoan parasites and mammalian cells. Overview 3D information is obtained by stereo imaging while complete 3D microscopy is provided by full tomographic reconstruction. The laboratory microscope image quality approaches that of the synchrotron microscopes, but with longer exposure times. The experimental image quality is analyzed from a numerical wave-propagation model of the imaging system and a path to reach synchrotron-like exposure times in laboratory microscopy is outlined.
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Affiliation(s)
- H M Hertz
- Biomedical and X-Ray Physics, Dept. of Applied Physics, KTH Royal Inst. of Technology/Albanova, 10691 Stockholm, Sweden.
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Bertilson M, von Hofsten O, Vogt U, Holmberg A, Christakou AE, Hertz HM. Laboratory soft-x-ray microscope for cryotomography of biological specimens. OPTICS LETTERS 2011; 36:2728-30. [PMID: 21765523 DOI: 10.1364/ol.36.002728] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Soft-x-ray cryotomography allows quantitative and high-resolution three-dimensional imaging of intact unstained cells. To date, the method relies on synchrotron-radiation sources, which limits accessibility for researchers. Here we present a laboratory water-window microscope for cryotomography. It is based on a λ=2.48 nm liquid-jet laser-plasma source, a normal-incidence multilayer condenser, a 30 nm zone-plate objective, and a cryotilt sample holder. We demonstrate high-resolution imaging, as well as quantitative tomographic imaging, of frozen intact cells. The reconstructed tomogram of the intracellular local absorption coefficient shows details down to ∼100 nm.
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Affiliation(s)
- Michael Bertilson
- Biomedical and X-Ray Physics, Department of Applied Physics, KTH Royal Institute of Technology/AlbaNova, 10691 Stockholm, Sweden
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