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Hong YP, Gleber SC, O’Halloran TV, Que EL, Bleher R, Vogt S, Woodruff TK, Jacobsen C. Alignment of low-dose X-ray fluorescence tomography images using differential phase contrast. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:229-34. [PMID: 24365941 PMCID: PMC3874022 DOI: 10.1107/s1600577513029512] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 10/25/2013] [Indexed: 05/09/2023]
Abstract
X-ray fluorescence nanotomography provides unprecedented sensitivity for studies of trace metal distributions in whole biological cells. Dose fractionation, in which one acquires very low dose individual projections and then obtains high statistics reconstructions as signal from a voxel is brought together (Hegerl & Hoppe, 1976), requires accurate alignment of these individual projections so as to correct for rotation stage runout. It is shown here that differential phase contrast at 10.2 keV beam energy offers the potential for accurate cross-correlation alignment of successive projections, by demonstrating that successive low dose, 3 ms per pixel, images acquired at the same specimen position and rotation angle have a narrower and smoother cross-correlation function (1.5 pixels FWHM at 300 nm pixel size) than that obtained from zinc fluorescence images (25 pixels FWHM). The differential phase contrast alignment resolution is thus well below the 700 nm × 500 nm beam spot size used in this demonstration, so that dose fractionation should be possible for reduced-dose, more rapidly acquired, fluorescence nanotomography experiments.
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Affiliation(s)
- Young Pyo Hong
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Correspondence e-mail:
| | - Sophie-Charlotte Gleber
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Thomas V. O’Halloran
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Emily L. Que
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Reiner Bleher
- Department of Materials Science and Engineering, 2220 Campus Drive, Evanston, IL 60208, USA
| | - Stefan Vogt
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Teresa K. Woodruff
- Department of Obstetrics and Gynecology, Northwestern University, 303 East Superior Street, Chicago, IL 60611, USA
| | - Chris Jacobsen
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
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2
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Krejci MR, Wasserman B, Finney L, McNulty I, Legnini D, Vogt S, Joester D. Selectivity in biomineralization of barium and strontium. J Struct Biol 2011; 176:192-202. [DOI: 10.1016/j.jsb.2011.08.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 08/05/2011] [Accepted: 08/05/2011] [Indexed: 10/17/2022]
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Hornberger B, de Jonge MD, Feser M, Holl P, Holzner C, Jacobsen C, Legnini D, Paterson D, Rehak P, Strüder L, Vogt S. Differential phase contrast with a segmented detector in a scanning X-ray microprobe. JOURNAL OF SYNCHROTRON RADIATION 2008; 15:355-62. [PMID: 18552427 PMCID: PMC3089014 DOI: 10.1107/s0909049508008509] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 03/29/2008] [Indexed: 05/09/2023]
Abstract
Scanning X-ray microprobes are unique tools for the nanoscale investigation of specimens from the life, environmental, materials and other fields of sciences. Typically they utilize absorption and fluorescence as contrast mechanisms. Phase contrast is a complementary technique that can provide strong contrast with reduced radiation dose for weakly absorbing structures in the multi-keV range. In this paper the development of a segmented charge-integrating silicon detector which provides simultaneous absorption and differential phase contrast is reported. The detector can be used together with a fluorescence detector for the simultaneous acquisition of transmission and fluorescence data. It can be used over a wide range of photon energies, photon rates and exposure times at third-generation synchrotron radiation sources, and is currently operating at two beamlines at the Advanced Photon Source. Images obtained at around 2 keV and 10 keV demonstrate the superiority of phase contrast over absorption for specimens composed of light elements.
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Affiliation(s)
- B Hornberger
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800, USA.
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4
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de Jonge MD, Hornberger B, Holzner C, Legnini D, Paterson D, McNulty I, Jacobsen C, Vogt S. Quantitative phase imaging with a scanning transmission x-ray microscope. PHYSICAL REVIEW LETTERS 2008; 100:163902. [PMID: 18518198 PMCID: PMC2860456 DOI: 10.1103/physrevlett.100.163902] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 02/13/2008] [Indexed: 05/20/2023]
Abstract
We obtain quantitative phase reconstructions from differential phase contrast images obtained with a scanning transmission x-ray microscope and 2.5 keV x rays. The theoretical basis of the technique is presented along with measurements and their interpretation.
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Affiliation(s)
- M D de Jonge
- Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA.
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5
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de Jonge MD, Vogt S, Legnini D, McNulty I, Rau C, Paterson D, Hornberger B, Holzner C, Jacobsen C. A method for phase reconstruction from measurements obtained using a configured detector with a scanning transmission X-ray microscope. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH. SECTION A, ACCELERATORS, SPECTROMETERS, DETECTORS AND ASSOCIATED EQUIPMENT 2007; 582:218-220. [PMID: 18843383 PMCID: PMC2562734 DOI: 10.1016/j.nima.2007.08.111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We developed a technique for performing quantitative phase reconstructions from differential phase contrast images obtained using a configured detector in a scanning transmission X-ray microscope geometry. The technique uses geometric optics to describe the interaction of the X-ray beam with the specimen, which allows interpretation of the measured intensities in terms of the derivative of the phase thickness. Integration of the resulting directional derivatives is performed using a Fourier integration technique. We demonstrate the approach by reconstructing simulated measurements of a 0.5-µm-diameter gold sphere at 7-keV photon energy.
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Affiliation(s)
- Martin D. de Jonge
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439-4856, USA
- Corresponding author. E-mail address: (M.D. de Jonge)
| | - Stefan Vogt
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439-4856, USA
| | - Daniel Legnini
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439-4856, USA
| | - Ian McNulty
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439-4856, USA
| | - Christoph Rau
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX 11 0DE, United Kingdom
| | - David Paterson
- Australian Synchrotron, 800 Blackburn Road, Clayton, Vic. 3168, Australia
| | - Benjamin Hornberger
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800, USA
| | - Christian Holzner
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800, USA
| | - Chris Jacobsen
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800, USA
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6
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de Jonge MD, Vogt S, Legnini D, McNulty I, Rau C, Paterson D, Hornberger B, Holzner C, Jacobsen C. A method for phase reconstruction from measurements obtained using a configured detector with a scanning transmission X-ray microscope. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH. SECTION A, ACCELERATORS, SPECTROMETERS, DETECTORS AND ASSOCIATED EQUIPMENT 2007. [PMID: 18843383 DOI: 10.1016/j.nima.2007.07.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We developed a technique for performing quantitative phase reconstructions from differential phase contrast images obtained using a configured detector in a scanning transmission X-ray microscope geometry. The technique uses geometric optics to describe the interaction of the X-ray beam with the specimen, which allows interpretation of the measured intensities in terms of the derivative of the phase thickness. Integration of the resulting directional derivatives is performed using a Fourier integration technique. We demonstrate the approach by reconstructing simulated measurements of a 0.5-µm-diameter gold sphere at 7-keV photon energy.
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Affiliation(s)
- Martin D de Jonge
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439-4856, USA
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