Implementation of a fast method for high resolution
phase contrast tomography

doi:10.1364/OE.14.008103

Implementation of a fast method for high resolution phase contrast tomography

A. Groso, R. Abela, and M. Stampanoni »View Author Affiliations

Optics Express, Vol. 14, Issue 18, pp. 8103-8110 (2006)
http://dx.doi.org/10.1364/OE.14.008103

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Abstract

We report the implementation of a method which can yield the 3D distribution of the phase (refractive index) of a weakly absorbing object from a single tomographic data set. In order to reduce the residual absorption artifact (due to the fact that only one data set is used) the original algorithm presented by A. V. Bronnikov is amended by adding in the filter a factor found by using a semi empirical approach. The quality of the reconstruction is largely sufficient for optimal segmentation and further postprocessing even though the filter correction is based on assumption of constant absorption. This one step approach allows keeping radiation dose to the minimum. Spatial resolution is comparable to the conventional absorption based technique. The performance of the method is validated by using an established phase contrast technique.

OCIS Codes
(100.5070) Image processing : Phase retrieval
(170.6960) Medical optics and biotechnology : Tomography
(340.7440) X-ray optics : X-ray imaging

ToC Category:
Image Processing

History
Original Manuscript: June 20, 2006
Revised Manuscript: August 21, 2006
Manuscript Accepted: August 23, 2006
Published: September 1, 2006

Virtual Issues
Vol. 1, Iss. 10 Virtual Journal for Biomedical Optics

Citation
A. Groso, R. Abela, and M. Stampanoni, "Implementation of a fast method for high resolution phase contrast tomography," Opt. Express 14, 8103-8110 (2006)
http://www.opticsinfobase.org/oe/abstract.cfm?URI=oe-14-18-8103

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References

U. Bonse and F. Bush, "X-ray computed microtomography using synchrotron radiation," Prog. Biophys. Mol. Biol., 65, 133-169 (1996). [CrossRef] [PubMed]
B. A. Dowd, G. H. H. H. Campbell, R. B. Marr, V. V. Nagarkar, S. V. Tipnis, L. Axe and D. P. Siddons, "Developments in synchrotron x-ray computed microtomography at the National Synchrotron Light Source," in Developments in X-Ray Tomography II, U. Bonse, ed., Proc. SPIE 3772, 224-236 (1999). [CrossRef]
M. Stampanoni, G. Borchert, P. Wyss, R. Abela, B. Patterson, S. Hunt, D. Vermeulen and P. Rüegsegger, "High resolution X-ray detector for synchrotron-based microtomography," Nucl Instrum Methods A 491,291-301 (2002). [CrossRef]
T. Weitkamp, C. Raven, and A. Snigirev, "An imaging and microtomography facility at the ESRF beamline ID 22," in Developments in X-Ray Tomography II, U. Bonse, ed., Proc. SPIE 3772, 311-317 (1999). [CrossRef]
U. Bonse and M. Hart, "An x-ray interferometer," Appl. Phys. Lett. 6, 155-156 (1965). [CrossRef]
U. Bonse, and F. Beckmann, "Multiple-beam X-ray interferometry for phase-contrast microtomography," Journal of Synchrotron Radiat. 8, 1-5 (2001). [CrossRef]
A. Momose, "Demonstration of phase-contrast x-ray computed-tomography using an x-ray interferometer," Nuclear Instruments and Methods A 352, 622-628 (1995). [CrossRef]
T. Weitkamp, A. Diaz, C. David, F. Pfeiffer, M. Stampanoni, P. Cloetens, and E. Ziegler, "X-ray phase imaging with a grating interferometer," Opt. Express 13, 6296-6304 (2005). [CrossRef] [PubMed]
M. R. Teague, "Deterministic phase retrieval - a Green-function solution," J. of the Opt. Soc. Am. 73, 1434-1441 (1983). [CrossRef]
K. A. Nugent, T. E. Gureyev, D. F. Cookson, D. Paganin, and Z. Barnea, "Quantitative phase imaging using hard x rays," Phys. Rev. Lett. 77, 2961-2964 (1996). [CrossRef] [PubMed]
L. J. Allen, W. McBride, N. L. O’Leary, and M. P. Oxley, "Exit wave reconstruction at atomic resolution," Ultramicroscopy 100, 91-104 (2004). [CrossRef] [PubMed]
W. K. Hsieh, F. R. Chen, J. J. Kai, A. I. Kirkland, "Resolution extension and exit wave reconstruction in complex HREM," Ultramicroscopy 98, 99-114 (2004). [CrossRef] [PubMed]
S. C. Mayo, P. R. Miller, S. W. Wilkins, T. J. Davis, D. Gao, T. E. Gureyev, D. Paganin, D. J. Parry, A. Pogany and A. W. Stevenson, "Quantitative X-ray projection microscopy: phase-contrast and multi-spectral imaging," J. Microsc. 207,79-96 (2002). [CrossRef] [PubMed]
T. E. Gureyev, A. Pogany, D. M. Paganin and S. W. Wilkins, "Linear algorithms for phase retrieval in the Fresnel region," Optics Commun. 231,53-70 (2004). [CrossRef]
A. G. Peele, F. DeCarlo, P. J. Mahon, B. B. Dhal and K. A. Nugent, "X-ray phase contrast tomography with a bending magnet source," Rev. Sci. Instrum. 76, 083707 (2005). [CrossRef]
T. E. Gureyev and K. A. Nugent, "Phase retrieval with the transport-of-intensity equation II. Orthogonal series solution for nonuniform illumination," J. Opt. Soc. Am. A 13, 1670-1682 (1996). [CrossRef]
P. Cloetens, W. Ludwig, J. Baruchel, D. Van Dyck, J. Van Landuyt, J. P. Guigay and M. Schlenker, "Holotomography: Quantitative phase tomography with micrometer resolution using hard synchrotron radiation x rays," Appl. Phys. Lett. 75,2912-2914 (1999). [CrossRef]
U. Bonse, F. Beckmann, M. Bartscher, T. Biermann, F. Busch, and O. Günnewig, "Phase contrast x-ray tomography using synchrotron radiation" in Developments in X-Ray Tomography, U. Bonse, ed., Proc. SPIE 3149, 108-119 (1997). [CrossRef]
A. V. Bronnikov, "Reconstruction formulas in phase-contrast tomography," Optics Communications 171, 239-244 (1999). [CrossRef]
A. V. Bronnikov, "Theory of quantitative phase-contrast computed tomography," J. of the Opt. Soc. of Am. A 19, 472-480 (2002). [CrossRef]
A. Groso, M. Stampanoni, R. Abela, P. Schneider, S. Linga, and R. Müller, "Phase contrast tomography: an alternative approach," Appl. Phys. Lett. 88, 214104 (2006). [CrossRef]
The computation of the two-dimensional Radon transform and backprojection over the angle ω are combined in a single step of the algorithm [20].
J. M. Cowley, Diffraction Physics (North-Holland, 1995), Chap. 3.4.
A. Pogany, D. Gao, and S. W. Wilkins, "Contrast and resolution in imaging with a microfocus x-ray source," Rev. Sci. Instr. 68,2774-2782 (1997). [CrossRef]

Abela, R.
Allen, L. J.
Barnea, Z.
Baruchel, J.
Beckmann, F.
Bonse, U.
Borchert, G.
Bronnikov, A. V.
Bush, F.
Chen, F. R.
Cloetens, P.
Cookson, D. F.
David, C.
Davis, T. J.
DeCarlo, F.
Dhal, B. B.
Diaz, A.
Gao, D.
Groso, A.
Guigay, J. P.
Gureyev, T. E.
Hart, M.
Hsieh, W. K.
Hunt, S.
Kai, J. J.
Kirkland, A. I.
Linga, S.
Ludwig, W.
Mahon, P. J.
Mayo, S. C.
McBride, W.
Miller, P. R.
Momose, A.
Müller, R.
Nugent, K. A.
O’Leary, N. L.
Oxley, M. P.
Paganin, D.
Paganin, D. M.
Parry, D. J.
Patterson, B.
Peele, A. G.
Pfeiffer, F.
Pogany, A.
Rüegsegger, P.
Schlenker, M.
Schneider, P.
Stampanoni, M.
Stevenson, A. W.
Teague, M. R.
Van Dyck, D.
Van Landuyt, J.
Vermeulen, D.
Weitkamp, T.
Wilkins, S. W.
Wyss, P.
Ziegler, E.

Appl. Phys. Lett.

U. Bonse and M. Hart, "An x-ray interferometer," Appl. Phys. Lett. 6, 155-156 (1965). [CrossRef]
P. Cloetens, W. Ludwig, J. Baruchel, D. Van Dyck, J. Van Landuyt, J. P. Guigay and M. Schlenker, "Holotomography: Quantitative phase tomography with micrometer resolution using hard synchrotron radiation x rays," Appl. Phys. Lett. 75,2912-2914 (1999). [CrossRef]
A. Groso, M. Stampanoni, R. Abela, P. Schneider, S. Linga, and R. Müller, "Phase contrast tomography: an alternative approach," Appl. Phys. Lett. 88, 214104 (2006). [CrossRef]

J. Microsc.

S. C. Mayo, P. R. Miller, S. W. Wilkins, T. J. Davis, D. Gao, T. E. Gureyev, D. Paganin, D. J. Parry, A. Pogany and A. W. Stevenson, "Quantitative X-ray projection microscopy: phase-contrast and multi-spectral imaging," J. Microsc. 207,79-96 (2002). [CrossRef] [PubMed]

J. of the Opt. Soc. Am.

M. R. Teague, "Deterministic phase retrieval - a Green-function solution," J. of the Opt. Soc. Am. 73, 1434-1441 (1983). [CrossRef]

J. of the Opt. Soc. of Am. A

A. V. Bronnikov, "Theory of quantitative phase-contrast computed tomography," J. of the Opt. Soc. of Am. A 19, 472-480 (2002). [CrossRef]

J. Opt. Soc. Am. A

T. E. Gureyev and K. A. Nugent, "Phase retrieval with the transport-of-intensity equation II. Orthogonal series solution for nonuniform illumination," J. Opt. Soc. Am. A 13, 1670-1682 (1996). [CrossRef]

Journal of Synchrotron Radiat.

U. Bonse, and F. Beckmann, "Multiple-beam X-ray interferometry for phase-contrast microtomography," Journal of Synchrotron Radiat. 8, 1-5 (2001). [CrossRef]

Nucl Instrum Methods A

M. Stampanoni, G. Borchert, P. Wyss, R. Abela, B. Patterson, S. Hunt, D. Vermeulen and P. Rüegsegger, "High resolution X-ray detector for synchrotron-based microtomography," Nucl Instrum Methods A 491,291-301 (2002). [CrossRef]

Nuclear Instruments and Methods A

A. Momose, "Demonstration of phase-contrast x-ray computed-tomography using an x-ray interferometer," Nuclear Instruments and Methods A 352, 622-628 (1995). [CrossRef]

Opt. Express

T. Weitkamp, A. Diaz, C. David, F. Pfeiffer, M. Stampanoni, P. Cloetens, and E. Ziegler, "X-ray phase imaging with a grating interferometer," Opt. Express 13, 6296-6304 (2005). [CrossRef] [PubMed]

Optics Commun.

T. E. Gureyev, A. Pogany, D. M. Paganin and S. W. Wilkins, "Linear algorithms for phase retrieval in the Fresnel region," Optics Commun. 231,53-70 (2004). [CrossRef]

Optics Communications

A. V. Bronnikov, "Reconstruction formulas in phase-contrast tomography," Optics Communications 171, 239-244 (1999). [CrossRef]

Phys. Rev. Lett.

K. A. Nugent, T. E. Gureyev, D. F. Cookson, D. Paganin, and Z. Barnea, "Quantitative phase imaging using hard x rays," Phys. Rev. Lett. 77, 2961-2964 (1996). [CrossRef] [PubMed]

Prog. Biophys. Mol. Biol.

U. Bonse and F. Bush, "X-ray computed microtomography using synchrotron radiation," Prog. Biophys. Mol. Biol., 65, 133-169 (1996). [CrossRef] [PubMed]

Rev. Sci. Instr.

A. Pogany, D. Gao, and S. W. Wilkins, "Contrast and resolution in imaging with a microfocus x-ray source," Rev. Sci. Instr. 68,2774-2782 (1997). [CrossRef]

Rev. Sci. Instrum.

A. G. Peele, F. DeCarlo, P. J. Mahon, B. B. Dhal and K. A. Nugent, "X-ray phase contrast tomography with a bending magnet source," Rev. Sci. Instrum. 76, 083707 (2005). [CrossRef]

Ultramicroscopy

L. J. Allen, W. McBride, N. L. O’Leary, and M. P. Oxley, "Exit wave reconstruction at atomic resolution," Ultramicroscopy 100, 91-104 (2004). [CrossRef] [PubMed]
W. K. Hsieh, F. R. Chen, J. J. Kai, A. I. Kirkland, "Resolution extension and exit wave reconstruction in complex HREM," Ultramicroscopy 98, 99-114 (2004). [CrossRef] [PubMed]

Other

U. Bonse, F. Beckmann, M. Bartscher, T. Biermann, F. Busch, and O. Günnewig, "Phase contrast x-ray tomography using synchrotron radiation" in Developments in X-Ray Tomography, U. Bonse, ed., Proc. SPIE 3149, 108-119 (1997). [CrossRef]
B. A. Dowd, G. H. H. H. Campbell, R. B. Marr, V. V. Nagarkar, S. V. Tipnis, L. Axe and D. P. Siddons, "Developments in synchrotron x-ray computed microtomography at the National Synchrotron Light Source," in Developments in X-Ray Tomography II, U. Bonse, ed., Proc. SPIE 3772, 224-236 (1999). [CrossRef]
T. Weitkamp, C. Raven, and A. Snigirev, "An imaging and microtomography facility at the ESRF beamline ID 22," in Developments in X-Ray Tomography II, U. Bonse, ed., Proc. SPIE 3772, 311-317 (1999). [CrossRef]
The computation of the two-dimensional Radon transform and backprojection over the angle ω are combined in a single step of the algorithm [20].
J. M. Cowley, Diffraction Physics (North-Holland, 1995), Chap. 3.4.

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[1] U. Bonse and F. Bush, "X-ray computed microtomography using synchrotron radiation," Prog. Biophys. Mol. Biol., 65, 133-169 (1996). [CrossRef] [PubMed]

[2] B. A. Dowd, G. H. H. H. Campbell, R. B. Marr, V. V. Nagarkar, S. V. Tipnis, L. Axe and D. P. Siddons, "Developments in synchrotron x-ray computed microtomography at the National Synchrotron Light Source," in Developments in X-Ray Tomography II, U. Bonse, ed., Proc. SPIE 3772, 224-236 (1999). [CrossRef]

[3] M. Stampanoni, G. Borchert, P. Wyss, R. Abela, B. Patterson, S. Hunt, D. Vermeulen and P. Rüegsegger, "High resolution X-ray detector for synchrotron-based microtomography," Nucl Instrum Methods A 491,291-301 (2002). [CrossRef]

[4] T. Weitkamp, C. Raven, and A. Snigirev, "An imaging and microtomography facility at the ESRF beamline ID 22," in Developments in X-Ray Tomography II, U. Bonse, ed., Proc. SPIE 3772, 311-317 (1999). [CrossRef]

[5] U. Bonse and M. Hart, "An x-ray interferometer," Appl. Phys. Lett. 6, 155-156 (1965). [CrossRef]

[6] U. Bonse, and F. Beckmann, "Multiple-beam X-ray interferometry for phase-contrast microtomography," Journal of Synchrotron Radiat. 8, 1-5 (2001). [CrossRef]

[7] A. Momose, "Demonstration of phase-contrast x-ray computed-tomography using an x-ray interferometer," Nuclear Instruments and Methods A 352, 622-628 (1995). [CrossRef]

[8] T. Weitkamp, A. Diaz, C. David, F. Pfeiffer, M. Stampanoni, P. Cloetens, and E. Ziegler, "X-ray phase imaging with a grating interferometer," Opt. Express 13, 6296-6304 (2005). [CrossRef] [PubMed]

[9] M. R. Teague, "Deterministic phase retrieval - a Green-function solution," J. of the Opt. Soc. Am. 73, 1434-1441 (1983). [CrossRef]

[10] K. A. Nugent, T. E. Gureyev, D. F. Cookson, D. Paganin, and Z. Barnea, "Quantitative phase imaging using hard x rays," Phys. Rev. Lett. 77, 2961-2964 (1996). [CrossRef] [PubMed]

[11] L. J. Allen, W. McBride, N. L. O’Leary, and M. P. Oxley, "Exit wave reconstruction at atomic resolution," Ultramicroscopy 100, 91-104 (2004). [CrossRef] [PubMed]

[12] W. K. Hsieh, F. R. Chen, J. J. Kai, A. I. Kirkland, "Resolution extension and exit wave reconstruction in complex HREM," Ultramicroscopy 98, 99-114 (2004). [CrossRef] [PubMed]

[13] S. C. Mayo, P. R. Miller, S. W. Wilkins, T. J. Davis, D. Gao, T. E. Gureyev, D. Paganin, D. J. Parry, A. Pogany and A. W. Stevenson, "Quantitative X-ray projection microscopy: phase-contrast and multi-spectral imaging," J. Microsc. 207,79-96 (2002). [CrossRef] [PubMed]

[14] T. E. Gureyev, A. Pogany, D. M. Paganin and S. W. Wilkins, "Linear algorithms for phase retrieval in the Fresnel region," Optics Commun. 231,53-70 (2004). [CrossRef]

[15] A. G. Peele, F. DeCarlo, P. J. Mahon, B. B. Dhal and K. A. Nugent, "X-ray phase contrast tomography with a bending magnet source," Rev. Sci. Instrum. 76, 083707 (2005). [CrossRef]

[16] T. E. Gureyev and K. A. Nugent, "Phase retrieval with the transport-of-intensity equation II. Orthogonal series solution for nonuniform illumination," J. Opt. Soc. Am. A 13, 1670-1682 (1996). [CrossRef]

[17] P. Cloetens, W. Ludwig, J. Baruchel, D. Van Dyck, J. Van Landuyt, J. P. Guigay and M. Schlenker, "Holotomography: Quantitative phase tomography with micrometer resolution using hard synchrotron radiation x rays," Appl. Phys. Lett. 75,2912-2914 (1999). [CrossRef]

[18] U. Bonse, F. Beckmann, M. Bartscher, T. Biermann, F. Busch, and O. Günnewig, "Phase contrast x-ray tomography using synchrotron radiation" in Developments in X-Ray Tomography, U. Bonse, ed., Proc. SPIE 3149, 108-119 (1997). [CrossRef]

[19] A. V. Bronnikov, "Reconstruction formulas in phase-contrast tomography," Optics Communications 171, 239-244 (1999). [CrossRef]

[20] A. V. Bronnikov, "Theory of quantitative phase-contrast computed tomography," J. of the Opt. Soc. of Am. A 19, 472-480 (2002). [CrossRef]

[21] A. Groso, M. Stampanoni, R. Abela, P. Schneider, S. Linga, and R. Müller, "Phase contrast tomography: an alternative approach," Appl. Phys. Lett. 88, 214104 (2006). [CrossRef]

[22] The computation of the two-dimensional Radon transform and backprojection over the angle ω are combined in a single step of the algorithm [20].

[23] J. M. Cowley, Diffraction Physics (North-Holland, 1995), Chap. 3.4.

[24] A. Pogany, D. Gao, and S. W. Wilkins, "Contrast and resolution in imaging with a microfocus x-ray source," Rev. Sci. Instr. 68,2774-2782 (1997). [CrossRef]

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