Abstract

The study analyzes noise in X-ray in-line phase tomography in a biomedical context. The impact of noise on detection of iron oxide nanoparticles in mouse brain is assessed. The part of the noise due to the imaging system and the part due to biology are quantitatively expressed in a Neyman Pearson detection strategy with two models of noise. This represents a practical extension of previous work on noise in phase-contrast X-ray imaging which focused on the theoretical expression of the signal-to-noise ratio in mono-dimensional phantoms, taking account of the statistical noise of the imaging system only. We also report the impact of the phase retrieval step on detection performance. Taken together, this constitutes a general methodology of practical interest for quantitative extraction of information from X-ray in-line phase tomography, and is also relevant to assessment of contrast agents with a blob-like signature in high resolution imaging.

© 2013 OSA

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    [CrossRef] [PubMed]
  5. Y. I. Nesterets, S. W. Wilkins, T. E. Gureyev, A. Pogany, and A. W. Stevenson, “On the optimization of experimental parameters for X-ray in-line phase-contrast imaging,” Rev. Sci. Instrum.76, 093706 (2005).
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    [CrossRef] [PubMed]
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    [CrossRef]
  11. C.-Y. Chou and P.-Y. Huang, “Image reconstruction in phase-contrast tomography exploiting the second-order statistical properties of the projection data,” Opt. Express10, 24396–24410 (2011).
    [CrossRef]
  12. M. J. Kitchen, D. M. Paganin, R. A. Lewis, N. Yagi, and K. Uesugi, “Analysis of speckle patterns in phase-contrast images of lung tissue,” Nucl. Instrum. Methods Phys. Res., Sect. A548, 240–246 (2005).
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    [CrossRef] [PubMed]
  16. F. Goudail and P. Réfrégier, Statistical Image Processing Techniques for Noisy Images: An Application-Oriented Approach (Kluwer Academic, 2004).
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  18. V. Desestret, J.-C. Brisset, E. Devillard, S. Moucharrafie, S. Nataf, J. Honnorat, N. Nighoghossian, Y. Berthezène, and M. Wiart, “Early stage investigations of USPIO-induced signal changes after local cerebral ischemia in mice,” Stroke40, 1834–1841 (2009).
    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
  21. D. M. Paganin, S. C. Mayo, T. E. Gureyev, P. R. Miller, and S. W. Wilkins, “Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object,” J. Microsc.206, 33–40 (2002).
    [CrossRef] [PubMed]
  22. M. Salome, F. Peyrin, P. Cloetens, C. Odet, A. M. Laval-Jeantet, J. Baruchel, and P. Spanne, “A synchrotron radiation microtomography system for the analysis of trabecular bone samples,” Med. Phys.26, 2194–2204 (1999).
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  23. T. Lindeberg, “Detecting salient blob-like image structures and their scales with a scale space primal sketch: a method for focus-of attention,” Int. J. Comput. Vision11, 283–318 (1993).
    [CrossRef]
  24. M. Langer, P. Cloetens, and F. Peyrin, “Regularization of phase retrieval with phase attenuation duality for 3D holotomography,” IEEE Trans. Image Process.19, 2428–2436 (2010).
    [CrossRef] [PubMed]
  25. R. J. Dejus and M. Sanchez del Rio, “Xop: A graphical user interface for spectral calculations and X-ray optics utilities,” Rev. Sci. Instrum.67, 3356 (1996).
    [CrossRef]
  26. M. A. Beltran, D. M. Paganin, K. Uesugi, and M. J. Kitchen, “2D and 3D X-ray phase retrieval of multi-material objects using a single defocus distance,” Opt. Express18, 6423–6436 (2010).
    [CrossRef] [PubMed]
  27. T. Weitkamp, D. Haas, D. Wegrzynek, and A. Rack, “ANKAphase: Software for single-distance phase retrieval from inline X-ray phase-contrast radiographs,” J. Synchrotron Radiat.18, 617–629 (2011).
    [CrossRef] [PubMed]
  28. R. C. Chen, H. L. Xie, L. Rigon, R. Longo, E. Castelli, and T. Q. Xiao, “Phase retrieval in quantitative x-ray microtomography with a single sample-to-detector distance,” Opt. Lett.36, 1719–1721, (2011).
    [CrossRef] [PubMed]

2013

A. Bravin, P. Coan, and P. Suortti, “X-ray phase-contrast imaging: From pre-clinical applications towards clinics,” Phys. Med. Biol.58, R1–35 (2013).
[CrossRef]

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

2012

2011

R. C. Chen, H. L. Xie, L. Rigon, R. Longo, E. Castelli, and T. Q. Xiao, “Phase retrieval in quantitative x-ray microtomography with a single sample-to-detector distance,” Opt. Lett.36, 1719–1721, (2011).
[CrossRef] [PubMed]

T. Weitkamp, D. Haas, D. Wegrzynek, and A. Rack, “ANKAphase: Software for single-distance phase retrieval from inline X-ray phase-contrast radiographs,” J. Synchrotron Radiat.18, 617–629 (2011).
[CrossRef] [PubMed]

C.-Y. Chou and M. A. Anastasio, “Noise texture and signal detectability in propagation based x-ray phase-contrast tomography,” Med. Phys.37, 270–291 (2011).
[CrossRef]

C.-Y. Chou and P.-Y. Huang, “Image reconstruction in phase-contrast tomography exploiting the second-order statistical properties of the projection data,” Opt. Express10, 24396–24410 (2011).
[CrossRef]

2010

S. Titarenko, V. Titarenko, A. Kyrieleis, and P. J. Withers, “A priori information in a regularized sinogram-based method for removing ring artefacts in tomography,” J. Synchrotron Radiat.17, 540–549 (2010).
[CrossRef] [PubMed]

M. Langer, P. Cloetens, and F. Peyrin, “Regularization of phase retrieval with phase attenuation duality for 3D holotomography,” IEEE Trans. Image Process.19, 2428–2436 (2010).
[CrossRef] [PubMed]

F. Chauveau, S. Moucharrafie, M. Wiart, J.-C. Brisset, Y. Berthezene, and N. Nighoghossian, “In vivo MRI assessment of permanent middle cerebral artery occlusion by electrocoagulation: Pitfalls of procedure,” Exp. Transl. Stroke Med.2, 4–8 (2010).
[CrossRef] [PubMed]

M. A. Beltran, D. M. Paganin, K. Uesugi, and M. J. Kitchen, “2D and 3D X-ray phase retrieval of multi-material objects using a single defocus distance,” Opt. Express18, 6423–6436 (2010).
[CrossRef] [PubMed]

2009

C.-Y. Chou and M. A. Anastasio, “Influence of imaging geometry on noise texture in quantitative in-line X-ray phase-contrast imaging,” Opt. Express.17, 14466–14480 (2009).
[CrossRef] [PubMed]

V. Desestret, J.-C. Brisset, E. Devillard, S. Moucharrafie, S. Nataf, J. Honnorat, N. Nighoghossian, Y. Berthezène, and M. Wiart, “Early stage investigations of USPIO-induced signal changes after local cerebral ischemia in mice,” Stroke40, 1834–1841 (2009).
[CrossRef] [PubMed]

2008

2006

2005

Y. I. Nesterets, S. W. Wilkins, T. E. Gureyev, A. Pogany, and A. W. Stevenson, “On the optimization of experimental parameters for X-ray in-line phase-contrast imaging,” Rev. Sci. Instrum.76, 093706 (2005).
[CrossRef]

M. J. Kitchen, D. M. Paganin, R. A. Lewis, N. Yagi, and K. Uesugi, “Analysis of speckle patterns in phase-contrast images of lung tissue,” Nucl. Instrum. Methods Phys. Res., Sect. A548, 240–246 (2005).
[CrossRef]

2002

D. M. Paganin, S. C. Mayo, T. E. Gureyev, P. R. Miller, and S. W. Wilkins, “Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object,” J. Microsc.206, 33–40 (2002).
[CrossRef] [PubMed]

1999

M. Salome, F. Peyrin, P. Cloetens, C. Odet, A. M. Laval-Jeantet, J. Baruchel, and P. Spanne, “A synchrotron radiation microtomography system for the analysis of trabecular bone samples,” Med. Phys.26, 2194–2204 (1999).
[CrossRef] [PubMed]

1998

C. Raven, “Numerical removal of ring artifacts in microtomography,” Rev. Sci. Instrum.69, 2978–2980 (1998).
[CrossRef]

1996

R. J. Dejus and M. Sanchez del Rio, “Xop: A graphical user interface for spectral calculations and X-ray optics utilities,” Rev. Sci. Instrum.67, 3356 (1996).
[CrossRef]

1993

T. Lindeberg, “Detecting salient blob-like image structures and their scales with a scale space primal sketch: a method for focus-of attention,” Int. J. Comput. Vision11, 283–318 (1993).
[CrossRef]

Anastasio, M. A.

C.-Y. Chou and M. A. Anastasio, “Noise texture and signal detectability in propagation based x-ray phase-contrast tomography,” Med. Phys.37, 270–291 (2011).
[CrossRef]

C.-Y. Chou and M. A. Anastasio, “Influence of imaging geometry on noise texture in quantitative in-line X-ray phase-contrast imaging,” Opt. Express.17, 14466–14480 (2009).
[CrossRef] [PubMed]

Baruchel, J.

M. Salome, F. Peyrin, P. Cloetens, C. Odet, A. M. Laval-Jeantet, J. Baruchel, and P. Spanne, “A synchrotron radiation microtomography system for the analysis of trabecular bone samples,” Med. Phys.26, 2194–2204 (1999).
[CrossRef] [PubMed]

Beltran, M. A.

Berthezene, Y.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

F. Chauveau, S. Moucharrafie, M. Wiart, J.-C. Brisset, Y. Berthezene, and N. Nighoghossian, “In vivo MRI assessment of permanent middle cerebral artery occlusion by electrocoagulation: Pitfalls of procedure,” Exp. Transl. Stroke Med.2, 4–8 (2010).
[CrossRef] [PubMed]

Berthezène, Y.

V. Desestret, J.-C. Brisset, E. Devillard, S. Moucharrafie, S. Nataf, J. Honnorat, N. Nighoghossian, Y. Berthezène, and M. Wiart, “Early stage investigations of USPIO-induced signal changes after local cerebral ischemia in mice,” Stroke40, 1834–1841 (2009).
[CrossRef] [PubMed]

Boin, M.

Boistel, R.

M. Langer, R. Boistel, E. Pagot, P. Cloetens, and F. Peyrin, “X-ray in-line phase microtomography for biomedical applications,” in Microscopy: Science, Technology, Applications and Education, Microscopy Book Series, A. Méndez-Vilas and J. Díaz, eds. (Formatex, 2010), pp. 391–402.

Bravin, A.

Brisset, J.-C.

F. Chauveau, S. Moucharrafie, M. Wiart, J.-C. Brisset, Y. Berthezene, and N. Nighoghossian, “In vivo MRI assessment of permanent middle cerebral artery occlusion by electrocoagulation: Pitfalls of procedure,” Exp. Transl. Stroke Med.2, 4–8 (2010).
[CrossRef] [PubMed]

V. Desestret, J.-C. Brisset, E. Devillard, S. Moucharrafie, S. Nataf, J. Honnorat, N. Nighoghossian, Y. Berthezène, and M. Wiart, “Early stage investigations of USPIO-induced signal changes after local cerebral ischemia in mice,” Stroke40, 1834–1841 (2009).
[CrossRef] [PubMed]

Bulte, J. W.

J. W. Bulte and M. M. Modo, Nanoparticles in Biomedical Imaging (Springer, 2007).

Castelli, E.

Chabrol, A.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

Chauveau, F.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

F. Chauveau, S. Moucharrafie, M. Wiart, J.-C. Brisset, Y. Berthezene, and N. Nighoghossian, “In vivo MRI assessment of permanent middle cerebral artery occlusion by electrocoagulation: Pitfalls of procedure,” Exp. Transl. Stroke Med.2, 4–8 (2010).
[CrossRef] [PubMed]

Chen, R. C.

Cho, T.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

Chou, C.-Y.

C.-Y. Chou and P.-Y. Huang, “Image reconstruction in phase-contrast tomography exploiting the second-order statistical properties of the projection data,” Opt. Express10, 24396–24410 (2011).
[CrossRef]

C.-Y. Chou and M. A. Anastasio, “Noise texture and signal detectability in propagation based x-ray phase-contrast tomography,” Med. Phys.37, 270–291 (2011).
[CrossRef]

C.-Y. Chou and M. A. Anastasio, “Influence of imaging geometry on noise texture in quantitative in-line X-ray phase-contrast imaging,” Opt. Express.17, 14466–14480 (2009).
[CrossRef] [PubMed]

Cloetens, P.

M. Langer, P. Cloetens, and F. Peyrin, “Regularization of phase retrieval with phase attenuation duality for 3D holotomography,” IEEE Trans. Image Process.19, 2428–2436 (2010).
[CrossRef] [PubMed]

M. Langer, P. Cloetens, J.-P. Guigay, and F. Peyrin, “Quantitative comparison of direct phase retrieval algorithms in in-line phase tomography,” Med. Phys.35, 4556–4566 (2008).
[CrossRef] [PubMed]

M. Salome, F. Peyrin, P. Cloetens, C. Odet, A. M. Laval-Jeantet, J. Baruchel, and P. Spanne, “A synchrotron radiation microtomography system for the analysis of trabecular bone samples,” Med. Phys.26, 2194–2204 (1999).
[CrossRef] [PubMed]

M. Langer, R. Boistel, E. Pagot, P. Cloetens, and F. Peyrin, “X-ray in-line phase microtomography for biomedical applications,” in Microscopy: Science, Technology, Applications and Education, Microscopy Book Series, A. Méndez-Vilas and J. Díaz, eds. (Formatex, 2010), pp. 391–402.

Coan, P.

Dejus, R. J.

R. J. Dejus and M. Sanchez del Rio, “Xop: A graphical user interface for spectral calculations and X-ray optics utilities,” Rev. Sci. Instrum.67, 3356 (1996).
[CrossRef]

Desestret, V.

V. Desestret, J.-C. Brisset, E. Devillard, S. Moucharrafie, S. Nataf, J. Honnorat, N. Nighoghossian, Y. Berthezène, and M. Wiart, “Early stage investigations of USPIO-induced signal changes after local cerebral ischemia in mice,” Stroke40, 1834–1841 (2009).
[CrossRef] [PubMed]

Devillard, E.

V. Desestret, J.-C. Brisset, E. Devillard, S. Moucharrafie, S. Nataf, J. Honnorat, N. Nighoghossian, Y. Berthezène, and M. Wiart, “Early stage investigations of USPIO-induced signal changes after local cerebral ischemia in mice,” Stroke40, 1834–1841 (2009).
[CrossRef] [PubMed]

Diemoz, P. C.

Durand, A.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

Goudail, F.

F. Goudail and P. Réfrégier, Statistical Image Processing Techniques for Noisy Images: An Application-Oriented Approach (Kluwer Academic, 2004).

Guigay, J.-P.

M. Langer, P. Cloetens, J.-P. Guigay, and F. Peyrin, “Quantitative comparison of direct phase retrieval algorithms in in-line phase tomography,” Med. Phys.35, 4556–4566 (2008).
[CrossRef] [PubMed]

Gureyev, T. E.

T. E. Gureyev, Y. I. Nesterets, A. W. Stevenson, P. R. Miller, A. Pogany, and S. W. Wilkins, “Some simple rules for contrast, signal-to-noise and resolution in in-line X-ray phase-contrast imaging,” Opt. Express16, 3223–3241 (2008).
[CrossRef] [PubMed]

Y. I. Nesterets, S. W. Wilkins, T. E. Gureyev, A. Pogany, and A. W. Stevenson, “On the optimization of experimental parameters for X-ray in-line phase-contrast imaging,” Rev. Sci. Instrum.76, 093706 (2005).
[CrossRef]

D. M. Paganin, S. C. Mayo, T. E. Gureyev, P. R. Miller, and S. W. Wilkins, “Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object,” J. Microsc.206, 33–40 (2002).
[CrossRef] [PubMed]

Haas, D.

T. Weitkamp, D. Haas, D. Wegrzynek, and A. Rack, “ANKAphase: Software for single-distance phase retrieval from inline X-ray phase-contrast radiographs,” J. Synchrotron Radiat.18, 617–629 (2011).
[CrossRef] [PubMed]

Haibel, A.

Honnorat, J.

V. Desestret, J.-C. Brisset, E. Devillard, S. Moucharrafie, S. Nataf, J. Honnorat, N. Nighoghossian, Y. Berthezène, and M. Wiart, “Early stage investigations of USPIO-induced signal changes after local cerebral ischemia in mice,” Stroke40, 1834–1841 (2009).
[CrossRef] [PubMed]

Huang, P.-Y.

C.-Y. Chou and P.-Y. Huang, “Image reconstruction in phase-contrast tomography exploiting the second-order statistical properties of the projection data,” Opt. Express10, 24396–24410 (2011).
[CrossRef]

Kitchen, M. J.

M. A. Beltran, D. M. Paganin, K. Uesugi, and M. J. Kitchen, “2D and 3D X-ray phase retrieval of multi-material objects using a single defocus distance,” Opt. Express18, 6423–6436 (2010).
[CrossRef] [PubMed]

M. J. Kitchen, D. M. Paganin, R. A. Lewis, N. Yagi, and K. Uesugi, “Analysis of speckle patterns in phase-contrast images of lung tissue,” Nucl. Instrum. Methods Phys. Res., Sect. A548, 240–246 (2005).
[CrossRef]

Kyrieleis, A.

S. Titarenko, V. Titarenko, A. Kyrieleis, and P. J. Withers, “A priori information in a regularized sinogram-based method for removing ring artefacts in tomography,” J. Synchrotron Radiat.17, 540–549 (2010).
[CrossRef] [PubMed]

Langer, M.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

P. C. Diemoz, A. Bravin, M. Langer, and P. Coan, “Analytical and experimental determination of signal-to-noise ratio and figure of merit in three phase-contrast imaging techniques,” Opt. Express20, 27670–27690 (2012).
[CrossRef] [PubMed]

M. Langer, P. Cloetens, and F. Peyrin, “Regularization of phase retrieval with phase attenuation duality for 3D holotomography,” IEEE Trans. Image Process.19, 2428–2436 (2010).
[CrossRef] [PubMed]

M. Langer, P. Cloetens, J.-P. Guigay, and F. Peyrin, “Quantitative comparison of direct phase retrieval algorithms in in-line phase tomography,” Med. Phys.35, 4556–4566 (2008).
[CrossRef] [PubMed]

M. Langer, R. Boistel, E. Pagot, P. Cloetens, and F. Peyrin, “X-ray in-line phase microtomography for biomedical applications,” in Microscopy: Science, Technology, Applications and Education, Microscopy Book Series, A. Méndez-Vilas and J. Díaz, eds. (Formatex, 2010), pp. 391–402.

Laval-Jeantet, A. M.

M. Salome, F. Peyrin, P. Cloetens, C. Odet, A. M. Laval-Jeantet, J. Baruchel, and P. Spanne, “A synchrotron radiation microtomography system for the analysis of trabecular bone samples,” Med. Phys.26, 2194–2204 (1999).
[CrossRef] [PubMed]

Lewis, R. A.

M. J. Kitchen, D. M. Paganin, R. A. Lewis, N. Yagi, and K. Uesugi, “Analysis of speckle patterns in phase-contrast images of lung tissue,” Nucl. Instrum. Methods Phys. Res., Sect. A548, 240–246 (2005).
[CrossRef]

Lindeberg, T.

T. Lindeberg, “Detecting salient blob-like image structures and their scales with a scale space primal sketch: a method for focus-of attention,” Int. J. Comput. Vision11, 283–318 (1993).
[CrossRef]

Longo, R.

Marinescu, M.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

Mayo, S. C.

D. M. Paganin, S. C. Mayo, T. E. Gureyev, P. R. Miller, and S. W. Wilkins, “Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object,” J. Microsc.206, 33–40 (2002).
[CrossRef] [PubMed]

Miller, P. R.

T. E. Gureyev, Y. I. Nesterets, A. W. Stevenson, P. R. Miller, A. Pogany, and S. W. Wilkins, “Some simple rules for contrast, signal-to-noise and resolution in in-line X-ray phase-contrast imaging,” Opt. Express16, 3223–3241 (2008).
[CrossRef] [PubMed]

D. M. Paganin, S. C. Mayo, T. E. Gureyev, P. R. Miller, and S. W. Wilkins, “Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object,” J. Microsc.206, 33–40 (2002).
[CrossRef] [PubMed]

Modo, M. M.

J. W. Bulte and M. M. Modo, Nanoparticles in Biomedical Imaging (Springer, 2007).

Moucharrafie, S.

F. Chauveau, S. Moucharrafie, M. Wiart, J.-C. Brisset, Y. Berthezene, and N. Nighoghossian, “In vivo MRI assessment of permanent middle cerebral artery occlusion by electrocoagulation: Pitfalls of procedure,” Exp. Transl. Stroke Med.2, 4–8 (2010).
[CrossRef] [PubMed]

V. Desestret, J.-C. Brisset, E. Devillard, S. Moucharrafie, S. Nataf, J. Honnorat, N. Nighoghossian, Y. Berthezène, and M. Wiart, “Early stage investigations of USPIO-induced signal changes after local cerebral ischemia in mice,” Stroke40, 1834–1841 (2009).
[CrossRef] [PubMed]

Nataf, S.

V. Desestret, J.-C. Brisset, E. Devillard, S. Moucharrafie, S. Nataf, J. Honnorat, N. Nighoghossian, Y. Berthezène, and M. Wiart, “Early stage investigations of USPIO-induced signal changes after local cerebral ischemia in mice,” Stroke40, 1834–1841 (2009).
[CrossRef] [PubMed]

Nesterets, Y. I.

T. E. Gureyev, Y. I. Nesterets, A. W. Stevenson, P. R. Miller, A. Pogany, and S. W. Wilkins, “Some simple rules for contrast, signal-to-noise and resolution in in-line X-ray phase-contrast imaging,” Opt. Express16, 3223–3241 (2008).
[CrossRef] [PubMed]

Y. I. Nesterets, S. W. Wilkins, T. E. Gureyev, A. Pogany, and A. W. Stevenson, “On the optimization of experimental parameters for X-ray in-line phase-contrast imaging,” Rev. Sci. Instrum.76, 093706 (2005).
[CrossRef]

Nighoghossian, N.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

F. Chauveau, S. Moucharrafie, M. Wiart, J.-C. Brisset, Y. Berthezene, and N. Nighoghossian, “In vivo MRI assessment of permanent middle cerebral artery occlusion by electrocoagulation: Pitfalls of procedure,” Exp. Transl. Stroke Med.2, 4–8 (2010).
[CrossRef] [PubMed]

V. Desestret, J.-C. Brisset, E. Devillard, S. Moucharrafie, S. Nataf, J. Honnorat, N. Nighoghossian, Y. Berthezène, and M. Wiart, “Early stage investigations of USPIO-induced signal changes after local cerebral ischemia in mice,” Stroke40, 1834–1841 (2009).
[CrossRef] [PubMed]

Odet, C.

M. Salome, F. Peyrin, P. Cloetens, C. Odet, A. M. Laval-Jeantet, J. Baruchel, and P. Spanne, “A synchrotron radiation microtomography system for the analysis of trabecular bone samples,” Med. Phys.26, 2194–2204 (1999).
[CrossRef] [PubMed]

Olivier, C.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

Paganin, D. M.

M. A. Beltran, D. M. Paganin, K. Uesugi, and M. J. Kitchen, “2D and 3D X-ray phase retrieval of multi-material objects using a single defocus distance,” Opt. Express18, 6423–6436 (2010).
[CrossRef] [PubMed]

M. J. Kitchen, D. M. Paganin, R. A. Lewis, N. Yagi, and K. Uesugi, “Analysis of speckle patterns in phase-contrast images of lung tissue,” Nucl. Instrum. Methods Phys. Res., Sect. A548, 240–246 (2005).
[CrossRef]

D. M. Paganin, S. C. Mayo, T. E. Gureyev, P. R. Miller, and S. W. Wilkins, “Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object,” J. Microsc.206, 33–40 (2002).
[CrossRef] [PubMed]

D. M. Paganin, Coherent X-Ray Optics (OxfordScience, 2006).
[CrossRef]

Pagot, E.

M. Langer, R. Boistel, E. Pagot, P. Cloetens, and F. Peyrin, “X-ray in-line phase microtomography for biomedical applications,” in Microscopy: Science, Technology, Applications and Education, Microscopy Book Series, A. Méndez-Vilas and J. Díaz, eds. (Formatex, 2010), pp. 391–402.

Peyrin, F.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

M. Langer, P. Cloetens, and F. Peyrin, “Regularization of phase retrieval with phase attenuation duality for 3D holotomography,” IEEE Trans. Image Process.19, 2428–2436 (2010).
[CrossRef] [PubMed]

M. Langer, P. Cloetens, J.-P. Guigay, and F. Peyrin, “Quantitative comparison of direct phase retrieval algorithms in in-line phase tomography,” Med. Phys.35, 4556–4566 (2008).
[CrossRef] [PubMed]

M. Salome, F. Peyrin, P. Cloetens, C. Odet, A. M. Laval-Jeantet, J. Baruchel, and P. Spanne, “A synchrotron radiation microtomography system for the analysis of trabecular bone samples,” Med. Phys.26, 2194–2204 (1999).
[CrossRef] [PubMed]

M. Langer, R. Boistel, E. Pagot, P. Cloetens, and F. Peyrin, “X-ray in-line phase microtomography for biomedical applications,” in Microscopy: Science, Technology, Applications and Education, Microscopy Book Series, A. Méndez-Vilas and J. Díaz, eds. (Formatex, 2010), pp. 391–402.

Pogany, A.

T. E. Gureyev, Y. I. Nesterets, A. W. Stevenson, P. R. Miller, A. Pogany, and S. W. Wilkins, “Some simple rules for contrast, signal-to-noise and resolution in in-line X-ray phase-contrast imaging,” Opt. Express16, 3223–3241 (2008).
[CrossRef] [PubMed]

Y. I. Nesterets, S. W. Wilkins, T. E. Gureyev, A. Pogany, and A. W. Stevenson, “On the optimization of experimental parameters for X-ray in-line phase-contrast imaging,” Rev. Sci. Instrum.76, 093706 (2005).
[CrossRef]

Rack, A.

T. Weitkamp, D. Haas, D. Wegrzynek, and A. Rack, “ANKAphase: Software for single-distance phase retrieval from inline X-ray phase-contrast radiographs,” J. Synchrotron Radiat.18, 617–629 (2011).
[CrossRef] [PubMed]

Raven, C.

C. Raven, “Numerical removal of ring artifacts in microtomography,” Rev. Sci. Instrum.69, 2978–2980 (1998).
[CrossRef]

Réfrégier, P.

F. Goudail and P. Réfrégier, Statistical Image Processing Techniques for Noisy Images: An Application-Oriented Approach (Kluwer Academic, 2004).

Rigon, L.

Rositi, H.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

Salome, M.

M. Salome, F. Peyrin, P. Cloetens, C. Odet, A. M. Laval-Jeantet, J. Baruchel, and P. Spanne, “A synchrotron radiation microtomography system for the analysis of trabecular bone samples,” Med. Phys.26, 2194–2204 (1999).
[CrossRef] [PubMed]

Sanchez del Rio, M.

R. J. Dejus and M. Sanchez del Rio, “Xop: A graphical user interface for spectral calculations and X-ray optics utilities,” Rev. Sci. Instrum.67, 3356 (1996).
[CrossRef]

Spanne, P.

M. Salome, F. Peyrin, P. Cloetens, C. Odet, A. M. Laval-Jeantet, J. Baruchel, and P. Spanne, “A synchrotron radiation microtomography system for the analysis of trabecular bone samples,” Med. Phys.26, 2194–2204 (1999).
[CrossRef] [PubMed]

Stevenson, A. W.

T. E. Gureyev, Y. I. Nesterets, A. W. Stevenson, P. R. Miller, A. Pogany, and S. W. Wilkins, “Some simple rules for contrast, signal-to-noise and resolution in in-line X-ray phase-contrast imaging,” Opt. Express16, 3223–3241 (2008).
[CrossRef] [PubMed]

Y. I. Nesterets, S. W. Wilkins, T. E. Gureyev, A. Pogany, and A. W. Stevenson, “On the optimization of experimental parameters for X-ray in-line phase-contrast imaging,” Rev. Sci. Instrum.76, 093706 (2005).
[CrossRef]

Suortti, P.

A. Bravin, P. Coan, and P. Suortti, “X-ray phase-contrast imaging: From pre-clinical applications towards clinics,” Phys. Med. Biol.58, R1–35 (2013).
[CrossRef]

Titarenko, S.

S. Titarenko, V. Titarenko, A. Kyrieleis, and P. J. Withers, “A priori information in a regularized sinogram-based method for removing ring artefacts in tomography,” J. Synchrotron Radiat.17, 540–549 (2010).
[CrossRef] [PubMed]

Titarenko, V.

S. Titarenko, V. Titarenko, A. Kyrieleis, and P. J. Withers, “A priori information in a regularized sinogram-based method for removing ring artefacts in tomography,” J. Synchrotron Radiat.17, 540–549 (2010).
[CrossRef] [PubMed]

Uesugi, K.

M. A. Beltran, D. M. Paganin, K. Uesugi, and M. J. Kitchen, “2D and 3D X-ray phase retrieval of multi-material objects using a single defocus distance,” Opt. Express18, 6423–6436 (2010).
[CrossRef] [PubMed]

M. J. Kitchen, D. M. Paganin, R. A. Lewis, N. Yagi, and K. Uesugi, “Analysis of speckle patterns in phase-contrast images of lung tissue,” Nucl. Instrum. Methods Phys. Res., Sect. A548, 240–246 (2005).
[CrossRef]

Wegrzynek, D.

T. Weitkamp, D. Haas, D. Wegrzynek, and A. Rack, “ANKAphase: Software for single-distance phase retrieval from inline X-ray phase-contrast radiographs,” J. Synchrotron Radiat.18, 617–629 (2011).
[CrossRef] [PubMed]

Weitkamp, T.

T. Weitkamp, D. Haas, D. Wegrzynek, and A. Rack, “ANKAphase: Software for single-distance phase retrieval from inline X-ray phase-contrast radiographs,” J. Synchrotron Radiat.18, 617–629 (2011).
[CrossRef] [PubMed]

Wiart, M.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

F. Chauveau, S. Moucharrafie, M. Wiart, J.-C. Brisset, Y. Berthezene, and N. Nighoghossian, “In vivo MRI assessment of permanent middle cerebral artery occlusion by electrocoagulation: Pitfalls of procedure,” Exp. Transl. Stroke Med.2, 4–8 (2010).
[CrossRef] [PubMed]

V. Desestret, J.-C. Brisset, E. Devillard, S. Moucharrafie, S. Nataf, J. Honnorat, N. Nighoghossian, Y. Berthezène, and M. Wiart, “Early stage investigations of USPIO-induced signal changes after local cerebral ischemia in mice,” Stroke40, 1834–1841 (2009).
[CrossRef] [PubMed]

Wilkins, S. W.

T. E. Gureyev, Y. I. Nesterets, A. W. Stevenson, P. R. Miller, A. Pogany, and S. W. Wilkins, “Some simple rules for contrast, signal-to-noise and resolution in in-line X-ray phase-contrast imaging,” Opt. Express16, 3223–3241 (2008).
[CrossRef] [PubMed]

Y. I. Nesterets, S. W. Wilkins, T. E. Gureyev, A. Pogany, and A. W. Stevenson, “On the optimization of experimental parameters for X-ray in-line phase-contrast imaging,” Rev. Sci. Instrum.76, 093706 (2005).
[CrossRef]

D. M. Paganin, S. C. Mayo, T. E. Gureyev, P. R. Miller, and S. W. Wilkins, “Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object,” J. Microsc.206, 33–40 (2002).
[CrossRef] [PubMed]

Withers, P. J.

S. Titarenko, V. Titarenko, A. Kyrieleis, and P. J. Withers, “A priori information in a regularized sinogram-based method for removing ring artefacts in tomography,” J. Synchrotron Radiat.17, 540–549 (2010).
[CrossRef] [PubMed]

Xiao, T. Q.

Xie, H. L.

Yagi, N.

M. J. Kitchen, D. M. Paganin, R. A. Lewis, N. Yagi, and K. Uesugi, “Analysis of speckle patterns in phase-contrast images of lung tissue,” Nucl. Instrum. Methods Phys. Res., Sect. A548, 240–246 (2005).
[CrossRef]

Exp. Transl. Stroke Med.

F. Chauveau, S. Moucharrafie, M. Wiart, J.-C. Brisset, Y. Berthezene, and N. Nighoghossian, “In vivo MRI assessment of permanent middle cerebral artery occlusion by electrocoagulation: Pitfalls of procedure,” Exp. Transl. Stroke Med.2, 4–8 (2010).
[CrossRef] [PubMed]

IEEE Trans. Image Process.

M. Langer, P. Cloetens, and F. Peyrin, “Regularization of phase retrieval with phase attenuation duality for 3D holotomography,” IEEE Trans. Image Process.19, 2428–2436 (2010).
[CrossRef] [PubMed]

Int. J. Comput. Vision

T. Lindeberg, “Detecting salient blob-like image structures and their scales with a scale space primal sketch: a method for focus-of attention,” Int. J. Comput. Vision11, 283–318 (1993).
[CrossRef]

J. Microsc.

D. M. Paganin, S. C. Mayo, T. E. Gureyev, P. R. Miller, and S. W. Wilkins, “Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object,” J. Microsc.206, 33–40 (2002).
[CrossRef] [PubMed]

J. Synchrotron Radiat.

S. Titarenko, V. Titarenko, A. Kyrieleis, and P. J. Withers, “A priori information in a regularized sinogram-based method for removing ring artefacts in tomography,” J. Synchrotron Radiat.17, 540–549 (2010).
[CrossRef] [PubMed]

T. Weitkamp, D. Haas, D. Wegrzynek, and A. Rack, “ANKAphase: Software for single-distance phase retrieval from inline X-ray phase-contrast radiographs,” J. Synchrotron Radiat.18, 617–629 (2011).
[CrossRef] [PubMed]

Med. Phys.

M. Langer, P. Cloetens, J.-P. Guigay, and F. Peyrin, “Quantitative comparison of direct phase retrieval algorithms in in-line phase tomography,” Med. Phys.35, 4556–4566 (2008).
[CrossRef] [PubMed]

M. Salome, F. Peyrin, P. Cloetens, C. Odet, A. M. Laval-Jeantet, J. Baruchel, and P. Spanne, “A synchrotron radiation microtomography system for the analysis of trabecular bone samples,” Med. Phys.26, 2194–2204 (1999).
[CrossRef] [PubMed]

C.-Y. Chou and M. A. Anastasio, “Noise texture and signal detectability in propagation based x-ray phase-contrast tomography,” Med. Phys.37, 270–291 (2011).
[CrossRef]

Mol. Imaging Biol.

M. Marinescu, M. Langer, A. Durand, C. Olivier, A. Chabrol, H. Rositi, F. Chauveau, T. Cho, N. Nighoghossian, Y. Berthezene, F. Peyrin, and M. Wiart, “Synchrotron radiation micro-computed tomography as a new method to detect iron oxide nanoparticles in the brain,” Mol. Imaging Biol.15, 552–559 (2013).
[CrossRef] [PubMed]

Nucl. Instrum. Methods Phys. Res., Sect. A

M. J. Kitchen, D. M. Paganin, R. A. Lewis, N. Yagi, and K. Uesugi, “Analysis of speckle patterns in phase-contrast images of lung tissue,” Nucl. Instrum. Methods Phys. Res., Sect. A548, 240–246 (2005).
[CrossRef]

Opt. Express

Opt. Express.

C.-Y. Chou and M. A. Anastasio, “Influence of imaging geometry on noise texture in quantitative in-line X-ray phase-contrast imaging,” Opt. Express.17, 14466–14480 (2009).
[CrossRef] [PubMed]

Opt. Lett.

Phys. Med. Biol.

A. Bravin, P. Coan, and P. Suortti, “X-ray phase-contrast imaging: From pre-clinical applications towards clinics,” Phys. Med. Biol.58, R1–35 (2013).
[CrossRef]

Rev. Sci. Instrum.

Y. I. Nesterets, S. W. Wilkins, T. E. Gureyev, A. Pogany, and A. W. Stevenson, “On the optimization of experimental parameters for X-ray in-line phase-contrast imaging,” Rev. Sci. Instrum.76, 093706 (2005).
[CrossRef]

R. J. Dejus and M. Sanchez del Rio, “Xop: A graphical user interface for spectral calculations and X-ray optics utilities,” Rev. Sci. Instrum.67, 3356 (1996).
[CrossRef]

C. Raven, “Numerical removal of ring artifacts in microtomography,” Rev. Sci. Instrum.69, 2978–2980 (1998).
[CrossRef]

Stroke

V. Desestret, J.-C. Brisset, E. Devillard, S. Moucharrafie, S. Nataf, J. Honnorat, N. Nighoghossian, Y. Berthezène, and M. Wiart, “Early stage investigations of USPIO-induced signal changes after local cerebral ischemia in mice,” Stroke40, 1834–1841 (2009).
[CrossRef] [PubMed]

Other

F. Goudail and P. Réfrégier, Statistical Image Processing Techniques for Noisy Images: An Application-Oriented Approach (Kluwer Academic, 2004).

J. W. Bulte and M. M. Modo, Nanoparticles in Biomedical Imaging (Springer, 2007).

D. M. Paganin, Coherent X-Ray Optics (OxfordScience, 2006).
[CrossRef]

M. Langer, R. Boistel, E. Pagot, P. Cloetens, and F. Peyrin, “X-ray in-line phase microtomography for biomedical applications,” in Microscopy: Science, Technology, Applications and Education, Microscopy Book Series, A. Méndez-Vilas and J. Díaz, eds. (Formatex, 2010), pp. 391–402.

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Figures (9)

Fig. 1
Fig. 1

Image processing pipeline used in this study. Imaging is performed with 17.6 keV selected from undulator radiation using Al filters. The X-ray beam transmitted through the specimen is acquired on a detector using a LuAg scintillator screen, visible light optics, and a 2048×2048 CCD detector. The detector is positioned at 1 meter from the sample for in-line phase-contrast imaging. The 3D volume is a stack of 1,000 slices of 2048 × 2048 voxels and slice thickness is equal to pixel size (isotropic voxels) 8μm.

Fig. 2
Fig. 2

Visual inspection of the evolution of the contrasts for various values of the δ/β coefficient in the phase retrieval.The arrow points to δ/β = 321 the best value for linearity between grey level and phase.

Fig. 3
Fig. 3

Proposed scheme for the detection of iron oxide nanoparticles in IPT. The scale range is the typical size expected for the iron oxide nanoparticles when absorbed by macrophages i.e. [rmin = 16μm; rmax = 48μm]. A blob is detected for each local minimum in the detection maps. Restriction is made on the amplitude down to a given percentage of the amplitude of the smallest minimum. This percentage is arbitrarily set here as 60%. The process is applied slice by slice.

Fig. 4
Fig. 4

Regions defined as noise and signal: background noise N1 is taken in a region located outside the mouse brain. Lesion noise N2 is taken in a part of the lesion visibly free of iron oxide nanoparticles. Signal regions B are binary masks where structures judged as iron oxide nanoparticles are set at 1, with 0 elsewhere.

Fig. 5
Fig. 5

Illustration of the diversity of grey level distributions in the background noise N1 on four different slices of the same scan of mouse brain. The histogram corresponds to the distribution in the region of interest delineated by the solid line.

Fig. 6
Fig. 6

Statistical properties measured in the background noise N1. The different curves in the plots correspond to the 8 different mouse brains. (A) mean MN1 and (B) standard deviation σN1.

Fig. 7
Fig. 7

Performance for iron oxide nanoparticle detection as a function of noise amplitude with solid line for the lesion noise N2, dashed line for the background noise N1, and dotted line for the Gaussian white noise N3. (A) displays the average error Ercenter of the distance between the center of the true disk and the center of the detected one, (B) average error Erradius between the radius of the true disk and the radius of the detected one, (C) probability of good detection Pr(D1 | H1) and (D) probability of false alarm Pr(D1 | H0).

Fig. 8
Fig. 8

Fisher ratio FR of Eq. (6) as a function of the δ/β coefficient in the phase retrieval. Statistics computed on 18 lesions representing a total of 1,080 pixels for the signal and 272,700 pixels for the noise. The solid line stands for FR between nanoparticles and lesion and the dashed line represents FR between mouse brain lesion and surrounding healthy tissue.

Fig. 9
Fig. 9

Receiver operator curve (ROC) giving the probability of good detection of nanoparticles Pr(D1 | H1) as a function of the probability of false detection of nanoparticles Pr(D1 | H0) for various δ/β values in the IPT reconstruction algorithm. In panel A, the region corresponding to hypothesis H1 is segmented manually in a region displaying blob microstructures of size compatible with nanoparticles and the background corresponding to hypothesis H0 is the surrounding lesion free of nanoparticles. Likewise in panel B, but H1 is lesion and H0 is the surrounding healthy tissue. The ROC curves are superimposed in Panel B for δ/β = 321, 700 and 1250.

Equations (6)

Equations on this page are rendered with MathJax. Learn more.

n = 1 δ + i β ,
U = A 0 exp ( in 2 π λ x ) = A 0 exp ( i 2 π λ x ) exp ( i δ 2 π λ x ) exp ( β 2 π λ x ) .
S 1 ( x , y ) = B ( x , y ) × M B + σ N 1 × N 1 ( x , y ) ,
Er radius = | r true r ˜ | ,
Er center = ( x true x c ˜ ) 2 + ( y true y c ˜ ) 2 ,
F R = ( μ signal μ noise ) 2 σ signal 2 + σ noise 2 ,

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