Abstract

The reconstruction quality in the model-based optical tomography modalities can greatly benefit from a priori information of accurate tissue optical properties, which are difficult to be obtained in vivo with a conventional diffuse optical tomography (DOT) system alone. One of the solutions is to apply a priori anatomical structures obtained with anatomical imaging systems such as X-ray computed tomography (XCT) to constrain the reconstruction process of DOT. However, since X-ray offers low soft-tissue contrast, segmentation of abdominal organs from sole XCT images can be problematic. In order to overcome the challenges, the current study proposes a novel method of recovering a priori organ-oriented tissue optical properties, where anatomical structures of an in vivo mouse are approximately obtained by registering a standard anatomical atlas, i.e., the Digimouse, to the target XCT volume with the non-rigid image registration, and, in turn, employed to guide DOT for extracting the optical properties of inner organs. Simulative investigations have validated the methodological availability of such atlas-registration-based DOT strategy in revealing both a priori anatomical structures and optical properties. Further experiments have demonstrated the feasibility of the proposed method for acquiring the organ-oriented tissue optical properties of in vivo mice, making it as an efficient way of the reconstruction enhancement.

© 2016 Optical Society of America

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2016 (1)

J. Van de Velde, J. Wouters, T. Vercauteren, W. De Gersem, E. Achten, W. De Neve, and T. Van Hoof, “Optimal number of atlases and label fusion for automatic multi-atlas-based brachial plexus contouring in radiotherapy treatment planning,” Radiat. Oncol. 11(1), 1 (2016).
[Crossref] [PubMed]

2015 (2)

2014 (7)

B. Li, F. Maafi, R. Berti, P. Pouliot, E. Rhéaume, J. C. Tardif, and F. Lesage, “Hybrid FMT-MRI applied to in vivo atherosclerosis imaging,” Biomed. Opt. Express 5(5), 1664–1676 (2014).
[Crossref] [PubMed]

G. Zhang, F. Liu, H. Pu, W. He, J. Luo, and J. Bai, “A direct method with structural priors for imaging pharmacokinetic parameters in dynamic fluorescence molecular tomography,” IEEE Trans. Biomed. Eng. 61(3), 986–990 (2014).
[Crossref] [PubMed]

P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
[Crossref] [PubMed]

L. Wu, H. Zhao, X. Wang, X. Yi, W. Chen, and F. Gao, “Enhancement of fluorescence molecular tomography with structural-prior-based diffuse optical tomography: combating optical background uncertainty,” Appl. Opt. 53(30), 6970–6982 (2014).
[Crossref] [PubMed]

L. Wu, W. Wan, X. Wang, Z. Zhou, J. Li, L. Zhang, H. Zhao, and F. Gao, “Shape-parameterized diffuse optical tomography holds promise for sensitivity enhancement of fluorescence molecular tomography,” Biomed. Opt. Express 5(10), 3640–3659 (2014).
[Crossref] [PubMed]

X. Wu, A. T. Eggebrecht, S. L. Ferradal, J. P. Culver, and H. Dehghani, “Quantitative evaluation of atlas-based high-density diffuse optical tomography for imaging of the human visual cortex,” Biomed. Opt. Express 5(11), 3882–3900 (2014).
[Crossref] [PubMed]

Y. Zhang, L. Chang, C. Ceritoglu, J. Skranes, T. Ernst, S. Mori, M. I. Miller, and K. Oishi, “A Bayesian approach to the creation of a study-customized neonatal brain atlas,” Neuroimage 101, 256–267 (2014).
[Crossref] [PubMed]

2013 (2)

S. L. Jacques, “Optical properties of biological tissues: a review,” Phys. Med. Biol. 58(11), R37–R61 (2013).
[Crossref] [PubMed]

Y. Deng, X.-X. Zhang, Z.-Y. Luo, J. Xu, X.-Q. Yang, and Y.-Z. Meng, “H. gong, and Q.-M. Luo, “Image reconstruction algorithm for steady-state diffuse optical tomography with structural priori information,” Wuli Xuebao 62(1), 014202 (2013).

2012 (3)

J. F. P. J. Abascal, J. Aguirre, J. Chamorro-Servent, M. Schweiger, S. Arridge, J. Ripoll, J. J. Vaquero, and M. Desco, “Influence of absorption and scattering on the quantification of fluorescence diffuse optical tomography using normalized data,” J. Biomed. Opt. 17(3), 036013 (2012).
[Crossref] [PubMed]

A. Ale, V. Ermolayev, E. Herzog, C. Cohrs, M. H. de Angelis, and V. Ntziachristos, “FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography-X-ray computed tomography,” Nat. Methods 9(6), 615–620 (2012).
[Crossref] [PubMed]

H. Yi, D. Chen, X. Qu, K. Peng, X. Chen, Y. Zhou, J. Tian, and J. Liang, “Multilevel, hybrid regularization method for reconstruction of fluorescent molecular tomography,” Appl. Opt. 51(7), 975–986 (2012).
[Crossref] [PubMed]

2011 (1)

2010 (3)

2009 (3)

2008 (1)

2007 (3)

Y. Lin, H. Gao, O. Nalcioglu, and G. Gulsen, “Fluorescence diffuse optical tomography with functional and anatomical a priori information: feasibility study,” Phys. Med. Biol. 52(18), 5569–5585 (2007).
[Crossref] [PubMed]

P. K. Yalavarthy, B. W. Pogue, H. Dehghani, C. M. Carpenter, S. Jiang, and K. D. Paulsen, “Structural information within regularization matrices improves near infrared diffuse optical tomography,” Opt. Express 15(13), 8043–8058 (2007).
[Crossref] [PubMed]

B. Dogdas, D. Stout, A. F. Chatziioannou, and R. M. Leahy, “Digimouse: a 3D whole body mouse atlas from CT and cryosection data,” Phys. Med. Biol. 52(3), 577–587 (2007).
[Crossref] [PubMed]

2005 (2)

W. Cong, G. Wang, D. Kumar, Y. Liu, M. Jiang, L. Wang, E. Hoffman, G. McLennan, P. McCray, J. Zabner, and A. Cong, “Practical reconstruction method for bioluminescence tomography,” Opt. Express 13(18), 6756–6771 (2005).
[Crossref] [PubMed]

G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study,” Phys. Med. Biol. 50(17), 4225–4241 (2005).
[Crossref] [PubMed]

2004 (2)

A. Barjatya, “Block matching algorithms for motion estimation,” IEEE Trans. Evol. Comput. 8(3), 225–239 (2004).

W. P. Segars, B. M. W. Tsui, E. C. Frey, G. A. Johnson, and S. S. Berr, “Development of a 4-D digital mouse phantom for molecular imaging research,” Mol. Imaging Biol. 6(3), 149–159 (2004).
[Crossref] [PubMed]

2003 (1)

H. Chui and A. Rangarajan, “A new point matching algorithm for non-rigid registration,” Comput. Vis. Image Underst. 89(2), 114–141 (2003).
[Crossref]

2002 (3)

2001 (1)

M. Dhenain, S. W. Ruffins, and R. E. Jacobs, “Three-dimensional digital mouse atlas using high-resolution MRI,” Dev. Biol. 232(2), 458–470 (2001).
[Crossref] [PubMed]

1999 (2)

M. Schweiger and S. R. Arridge, “Optical tomographic reconstruction in a complex head model using a priori region boundary information,” Phys. Med. Biol. 44(11), 2703–2721 (1999).
[Crossref] [PubMed]

D. Rueckert, L. I. Sonoda, C. Hayes, D. L. G. Hill, M. O. Leach, and D. J. Hawkes, “Nonrigid registration using free-form deformations: application to breast MR images,” IEEE Trans. Med. Imaging 18(8), 712–721 (1999).
[Crossref] [PubMed]

1997 (1)

S. Lee, G. Wolberg, and S. Y. Shin, “Scattered data interpolation with multilevel B-splines,” IEEE Trans. Vis. Comput. Graph. 3(3), 228–244 (1997).
[Crossref]

1984 (1)

Abascal, J. F. P. J.

J. F. P. J. Abascal, J. Aguirre, J. Chamorro-Servent, M. Schweiger, S. Arridge, J. Ripoll, J. J. Vaquero, and M. Desco, “Influence of absorption and scattering on the quantification of fluorescence diffuse optical tomography using normalized data,” J. Biomed. Opt. 17(3), 036013 (2012).
[Crossref] [PubMed]

Achten, E.

J. Van de Velde, J. Wouters, T. Vercauteren, W. De Gersem, E. Achten, W. De Neve, and T. Van Hoof, “Optimal number of atlases and label fusion for automatic multi-atlas-based brachial plexus contouring in radiotherapy treatment planning,” Radiat. Oncol. 11(1), 1 (2016).
[Crossref] [PubMed]

Aguirre, J.

J. F. P. J. Abascal, J. Aguirre, J. Chamorro-Servent, M. Schweiger, S. Arridge, J. Ripoll, J. J. Vaquero, and M. Desco, “Influence of absorption and scattering on the quantification of fluorescence diffuse optical tomography using normalized data,” J. Biomed. Opt. 17(3), 036013 (2012).
[Crossref] [PubMed]

Ale, A.

A. Ale, V. Ermolayev, E. Herzog, C. Cohrs, M. H. de Angelis, and V. Ntziachristos, “FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography-X-ray computed tomography,” Nat. Methods 9(6), 615–620 (2012).
[Crossref] [PubMed]

Alexandrakis, G.

G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study,” Phys. Med. Biol. 50(17), 4225–4241 (2005).
[Crossref] [PubMed]

Arridge, S.

J. F. P. J. Abascal, J. Aguirre, J. Chamorro-Servent, M. Schweiger, S. Arridge, J. Ripoll, J. J. Vaquero, and M. Desco, “Influence of absorption and scattering on the quantification of fluorescence diffuse optical tomography using normalized data,” J. Biomed. Opt. 17(3), 036013 (2012).
[Crossref] [PubMed]

Arridge, S. R.

V. Y. Soloviev, C. D’Andrea, G. Valentini, R. Cubeddu, and S. R. Arridge, “Combined reconstruction of fluorescent and optical parameters using time-resolved data,” Appl. Opt. 48(1), 28–36 (2009).
[Crossref] [PubMed]

M. Schweiger and S. R. Arridge, “Optical tomographic reconstruction in a complex head model using a priori region boundary information,” Phys. Med. Biol. 44(11), 2703–2721 (1999).
[Crossref] [PubMed]

Bai, J.

G. Zhang, F. Liu, H. Pu, W. He, J. Luo, and J. Bai, “A direct method with structural priors for imaging pharmacokinetic parameters in dynamic fluorescence molecular tomography,” IEEE Trans. Biomed. Eng. 61(3), 986–990 (2014).
[Crossref] [PubMed]

Barber, W. C.

Barjatya, A.

A. Barjatya, “Block matching algorithms for motion estimation,” IEEE Trans. Evol. Comput. 8(3), 225–239 (2004).

Bech, M.

P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
[Crossref] [PubMed]

Berr, S. S.

W. P. Segars, B. M. W. Tsui, E. C. Frey, G. A. Johnson, and S. S. Berr, “Development of a 4-D digital mouse phantom for molecular imaging research,” Mol. Imaging Biol. 6(3), 149–159 (2004).
[Crossref] [PubMed]

Berti, R.

Brooks, D.

Burton, N. C.

P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
[Crossref] [PubMed]

Carpenter, C. M.

Ceritoglu, C.

Y. Zhang, L. Chang, C. Ceritoglu, J. Skranes, T. Ernst, S. Mori, M. I. Miller, and K. Oishi, “A Bayesian approach to the creation of a study-customized neonatal brain atlas,” Neuroimage 101, 256–267 (2014).
[Crossref] [PubMed]

Chamorro-Servent, J.

J. F. P. J. Abascal, J. Aguirre, J. Chamorro-Servent, M. Schweiger, S. Arridge, J. Ripoll, J. J. Vaquero, and M. Desco, “Influence of absorption and scattering on the quantification of fluorescence diffuse optical tomography using normalized data,” J. Biomed. Opt. 17(3), 036013 (2012).
[Crossref] [PubMed]

Chang, L.

Y. Zhang, L. Chang, C. Ceritoglu, J. Skranes, T. Ernst, S. Mori, M. I. Miller, and K. Oishi, “A Bayesian approach to the creation of a study-customized neonatal brain atlas,” Neuroimage 101, 256–267 (2014).
[Crossref] [PubMed]

Chatziioannou, A. F.

B. Dogdas, D. Stout, A. F. Chatziioannou, and R. M. Leahy, “Digimouse: a 3D whole body mouse atlas from CT and cryosection data,” Phys. Med. Biol. 52(3), 577–587 (2007).
[Crossref] [PubMed]

G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study,” Phys. Med. Biol. 50(17), 4225–4241 (2005).
[Crossref] [PubMed]

Chen, D.

Chen, W.

Chen, X.

Chui, H.

H. Chui and A. Rangarajan, “A new point matching algorithm for non-rigid registration,” Comput. Vis. Image Underst. 89(2), 114–141 (2003).
[Crossref]

Cohrs, C.

A. Ale, V. Ermolayev, E. Herzog, C. Cohrs, M. H. de Angelis, and V. Ntziachristos, “FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography-X-ray computed tomography,” Nat. Methods 9(6), 615–620 (2012).
[Crossref] [PubMed]

Cong, A.

Cong, W.

Cubeddu, R.

Culver, J. P.

D’Andrea, C.

Davis, L. C.

Davis, S. C.

F. Leblond, S. C. Davis, P. A. Valdés, and B. W. Pogue, “Pre-clinical whole-body fluorescence imaging: Review of instruments, methods and applications,” J. Photochem. Photobiol. B 98(1), 77–94 (2010).
[Crossref] [PubMed]

de Angelis, M. H.

A. Ale, V. Ermolayev, E. Herzog, C. Cohrs, M. H. de Angelis, and V. Ntziachristos, “FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography-X-ray computed tomography,” Nat. Methods 9(6), 615–620 (2012).
[Crossref] [PubMed]

De Gersem, W.

J. Van de Velde, J. Wouters, T. Vercauteren, W. De Gersem, E. Achten, W. De Neve, and T. Van Hoof, “Optimal number of atlases and label fusion for automatic multi-atlas-based brachial plexus contouring in radiotherapy treatment planning,” Radiat. Oncol. 11(1), 1 (2016).
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J. Van de Velde, J. Wouters, T. Vercauteren, W. De Gersem, E. Achten, W. De Neve, and T. Van Hoof, “Optimal number of atlases and label fusion for automatic multi-atlas-based brachial plexus contouring in radiotherapy treatment planning,” Radiat. Oncol. 11(1), 1 (2016).
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Deng, Y.

Y. Deng, X.-X. Zhang, Z.-Y. Luo, J. Xu, X.-Q. Yang, and Y.-Z. Meng, “H. gong, and Q.-M. Luo, “Image reconstruction algorithm for steady-state diffuse optical tomography with structural priori information,” Wuli Xuebao 62(1), 014202 (2013).

Desco, M.

J. F. P. J. Abascal, J. Aguirre, J. Chamorro-Servent, M. Schweiger, S. Arridge, J. Ripoll, J. J. Vaquero, and M. Desco, “Influence of absorption and scattering on the quantification of fluorescence diffuse optical tomography using normalized data,” J. Biomed. Opt. 17(3), 036013 (2012).
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M. Dhenain, S. W. Ruffins, and R. E. Jacobs, “Three-dimensional digital mouse atlas using high-resolution MRI,” Dev. Biol. 232(2), 458–470 (2001).
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B. Dogdas, D. Stout, A. F. Chatziioannou, and R. M. Leahy, “Digimouse: a 3D whole body mouse atlas from CT and cryosection data,” Phys. Med. Biol. 52(3), 577–587 (2007).
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El-Ghussein, F.

Ermolayev, V.

P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
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A. Ale, V. Ermolayev, E. Herzog, C. Cohrs, M. H. de Angelis, and V. Ntziachristos, “FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography-X-ray computed tomography,” Nat. Methods 9(6), 615–620 (2012).
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Ernst, T.

Y. Zhang, L. Chang, C. Ceritoglu, J. Skranes, T. Ernst, S. Mori, M. I. Miller, and K. Oishi, “A Bayesian approach to the creation of a study-customized neonatal brain atlas,” Neuroimage 101, 256–267 (2014).
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Ferradal, S. L.

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W. P. Segars, B. M. W. Tsui, E. C. Frey, G. A. Johnson, and S. S. Berr, “Development of a 4-D digital mouse phantom for molecular imaging research,” Mol. Imaging Biol. 6(3), 149–159 (2004).
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Gao, H.

Y. Lin, H. Gao, O. Nalcioglu, and G. Gulsen, “Fluorescence diffuse optical tomography with functional and anatomical a priori information: feasibility study,” Phys. Med. Biol. 52(18), 5569–5585 (2007).
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H. Dehghani, S. Srinivasan, B. W. Pogue, and A. Gibson, “Numerical modelling and image reconstruction in diffuse optical tomography,” Philos Trans A Math Phys Eng Sci 367(1900), 3073–3093 (2009).
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Y. Lin, W. C. Barber, J. S. Iwanczyk, W. Roeck, O. Nalcioglu, and G. Gulsen, “Quantitative fluorescence tomography using a combined tri-modality FT/DOT/XCT system,” Opt. Express 18(8), 7835–7850 (2010).
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Y. Lin, H. Gao, O. Nalcioglu, and G. Gulsen, “Fluorescence diffuse optical tomography with functional and anatomical a priori information: feasibility study,” Phys. Med. Biol. 52(18), 5569–5585 (2007).
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D. Rueckert, L. I. Sonoda, C. Hayes, D. L. G. Hill, M. O. Leach, and D. J. Hawkes, “Nonrigid registration using free-form deformations: application to breast MR images,” IEEE Trans. Med. Imaging 18(8), 712–721 (1999).
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D. Rueckert, L. I. Sonoda, C. Hayes, D. L. G. Hill, M. O. Leach, and D. J. Hawkes, “Nonrigid registration using free-form deformations: application to breast MR images,” IEEE Trans. Med. Imaging 18(8), 712–721 (1999).
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G. Zhang, F. Liu, H. Pu, W. He, J. Luo, and J. Bai, “A direct method with structural priors for imaging pharmacokinetic parameters in dynamic fluorescence molecular tomography,” IEEE Trans. Biomed. Eng. 61(3), 986–990 (2014).
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A. Ale, V. Ermolayev, E. Herzog, C. Cohrs, M. H. de Angelis, and V. Ntziachristos, “FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography-X-ray computed tomography,” Nat. Methods 9(6), 615–620 (2012).
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D. Rueckert, L. I. Sonoda, C. Hayes, D. L. G. Hill, M. O. Leach, and D. J. Hawkes, “Nonrigid registration using free-form deformations: application to breast MR images,” IEEE Trans. Med. Imaging 18(8), 712–721 (1999).
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P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
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Holt, R. W.

Hyde, D.

Iwanczyk, J. S.

Jacobs, R. E.

M. Dhenain, S. W. Ruffins, and R. E. Jacobs, “Three-dimensional digital mouse atlas using high-resolution MRI,” Dev. Biol. 232(2), 458–470 (2001).
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S. L. Jacques, “Optical properties of biological tissues: a review,” Phys. Med. Biol. 58(11), R37–R61 (2013).
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Jiang, M.

Jiang, S.

Johnson, G. A.

W. P. Segars, B. M. W. Tsui, E. C. Frey, G. A. Johnson, and S. S. Berr, “Development of a 4-D digital mouse phantom for molecular imaging research,” Mol. Imaging Biol. 6(3), 149–159 (2004).
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Klemm, U.

P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
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Kress, J. W.

Kumar, D.

Leach, M. O.

D. Rueckert, L. I. Sonoda, C. Hayes, D. L. G. Hill, M. O. Leach, and D. J. Hawkes, “Nonrigid registration using free-form deformations: application to breast MR images,” IEEE Trans. Med. Imaging 18(8), 712–721 (1999).
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Leahy, R. M.

B. Dogdas, D. Stout, A. F. Chatziioannou, and R. M. Leahy, “Digimouse: a 3D whole body mouse atlas from CT and cryosection data,” Phys. Med. Biol. 52(3), 577–587 (2007).
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F. Leblond, K. M. Tichauer, R. W. Holt, F. El-Ghussein, and B. W. Pogue, “Toward whole-body optical imaging of rats using single-photon counting fluorescence tomography,” Opt. Lett. 36(19), 3723–3725 (2011).
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F. Leblond, S. C. Davis, P. A. Valdés, and B. W. Pogue, “Pre-clinical whole-body fluorescence imaging: Review of instruments, methods and applications,” J. Photochem. Photobiol. B 98(1), 77–94 (2010).
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Lee, S.

S. Lee, G. Wolberg, and S. Y. Shin, “Scattered data interpolation with multilevel B-splines,” IEEE Trans. Vis. Comput. Graph. 3(3), 228–244 (1997).
[Crossref]

Lesage, F.

Li, B.

Li, J.

Liang, J.

Lin, Y.

Y. Lin, W. C. Barber, J. S. Iwanczyk, W. Roeck, O. Nalcioglu, and G. Gulsen, “Quantitative fluorescence tomography using a combined tri-modality FT/DOT/XCT system,” Opt. Express 18(8), 7835–7850 (2010).
[Crossref] [PubMed]

Y. Lin, H. Gao, O. Nalcioglu, and G. Gulsen, “Fluorescence diffuse optical tomography with functional and anatomical a priori information: feasibility study,” Phys. Med. Biol. 52(18), 5569–5585 (2007).
[Crossref] [PubMed]

Liu, F.

G. Zhang, F. Liu, H. Pu, W. He, J. Luo, and J. Bai, “A direct method with structural priors for imaging pharmacokinetic parameters in dynamic fluorescence molecular tomography,” IEEE Trans. Biomed. Eng. 61(3), 986–990 (2014).
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Liu, X.

X. Liu, Z.-Z. Yan, and H.-B. Lu, “Performance evaluation of a priori Information on reconstruction of fluorescence molecular tomography,” IEEE Access 3, 64–72 (2015).
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Liu, Y.

Lu, H.-B.

X. Liu, Z.-Z. Yan, and H.-B. Lu, “Performance evaluation of a priori Information on reconstruction of fluorescence molecular tomography,” IEEE Access 3, 64–72 (2015).
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Luo, J.

G. Zhang, F. Liu, H. Pu, W. He, J. Luo, and J. Bai, “A direct method with structural priors for imaging pharmacokinetic parameters in dynamic fluorescence molecular tomography,” IEEE Trans. Biomed. Eng. 61(3), 986–990 (2014).
[Crossref] [PubMed]

Luo, Z.-Y.

Y. Deng, X.-X. Zhang, Z.-Y. Luo, J. Xu, X.-Q. Yang, and Y.-Z. Meng, “H. gong, and Q.-M. Luo, “Image reconstruction algorithm for steady-state diffuse optical tomography with structural priori information,” Wuli Xuebao 62(1), 014202 (2013).

Ma, X.

P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
[Crossref] [PubMed]

Maafi, F.

Marschner, M.

P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
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McCray, P.

McLennan, G.

Meng, Y.-Z.

Y. Deng, X.-X. Zhang, Z.-Y. Luo, J. Xu, X.-Q. Yang, and Y.-Z. Meng, “H. gong, and Q.-M. Luo, “Image reconstruction algorithm for steady-state diffuse optical tomography with structural priori information,” Wuli Xuebao 62(1), 014202 (2013).

Miller, E.

Miller, M. I.

Y. Zhang, L. Chang, C. Ceritoglu, J. Skranes, T. Ernst, S. Mori, M. I. Miller, and K. Oishi, “A Bayesian approach to the creation of a study-customized neonatal brain atlas,” Neuroimage 101, 256–267 (2014).
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P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
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Mori, S.

Y. Zhang, L. Chang, C. Ceritoglu, J. Skranes, T. Ernst, S. Mori, M. I. Miller, and K. Oishi, “A Bayesian approach to the creation of a study-customized neonatal brain atlas,” Neuroimage 101, 256–267 (2014).
[Crossref] [PubMed]

Nalcioglu, O.

Y. Lin, W. C. Barber, J. S. Iwanczyk, W. Roeck, O. Nalcioglu, and G. Gulsen, “Quantitative fluorescence tomography using a combined tri-modality FT/DOT/XCT system,” Opt. Express 18(8), 7835–7850 (2010).
[Crossref] [PubMed]

Y. Lin, H. Gao, O. Nalcioglu, and G. Gulsen, “Fluorescence diffuse optical tomography with functional and anatomical a priori information: feasibility study,” Phys. Med. Biol. 52(18), 5569–5585 (2007).
[Crossref] [PubMed]

Ntziachristos, V.

P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
[Crossref] [PubMed]

A. Ale, V. Ermolayev, E. Herzog, C. Cohrs, M. H. de Angelis, and V. Ntziachristos, “FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography-X-ray computed tomography,” Nat. Methods 9(6), 615–620 (2012).
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D. Hyde, R. Schulz, D. Brooks, E. Miller, and V. Ntziachristos, “Performance dependence of hybrid x-ray computed tomography/fluorescence molecular tomography on the optical forward problem,” J. Opt. Soc. Am. A 26(4), 919–923 (2009).
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Y. Zhang, L. Chang, C. Ceritoglu, J. Skranes, T. Ernst, S. Mori, M. I. Miller, and K. Oishi, “A Bayesian approach to the creation of a study-customized neonatal brain atlas,” Neuroimage 101, 256–267 (2014).
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Paulsen, K. D.

Peng, K.

Pfeiffer, F.

P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
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Poulet, P.

Pouliot, P.

Pu, H.

G. Zhang, F. Liu, H. Pu, W. He, J. Luo, and J. Bai, “A direct method with structural priors for imaging pharmacokinetic parameters in dynamic fluorescence molecular tomography,” IEEE Trans. Biomed. Eng. 61(3), 986–990 (2014).
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Radrich, K.

P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
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H. Chui and A. Rangarajan, “A new point matching algorithm for non-rigid registration,” Comput. Vis. Image Underst. 89(2), 114–141 (2003).
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G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study,” Phys. Med. Biol. 50(17), 4225–4241 (2005).
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Rhéaume, E.

Ripoll, J.

J. F. P. J. Abascal, J. Aguirre, J. Chamorro-Servent, M. Schweiger, S. Arridge, J. Ripoll, J. J. Vaquero, and M. Desco, “Influence of absorption and scattering on the quantification of fluorescence diffuse optical tomography using normalized data,” J. Biomed. Opt. 17(3), 036013 (2012).
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Roeck, W.

Rueckert, D.

D. Rueckert, L. I. Sonoda, C. Hayes, D. L. G. Hill, M. O. Leach, and D. J. Hawkes, “Nonrigid registration using free-form deformations: application to breast MR images,” IEEE Trans. Med. Imaging 18(8), 712–721 (1999).
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M. Dhenain, S. W. Ruffins, and R. E. Jacobs, “Three-dimensional digital mouse atlas using high-resolution MRI,” Dev. Biol. 232(2), 458–470 (2001).
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Schulz, R.

Schweiger, M.

J. F. P. J. Abascal, J. Aguirre, J. Chamorro-Servent, M. Schweiger, S. Arridge, J. Ripoll, J. J. Vaquero, and M. Desco, “Influence of absorption and scattering on the quantification of fluorescence diffuse optical tomography using normalized data,” J. Biomed. Opt. 17(3), 036013 (2012).
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M. Schweiger and S. R. Arridge, “Optical tomographic reconstruction in a complex head model using a priori region boundary information,” Phys. Med. Biol. 44(11), 2703–2721 (1999).
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W. P. Segars, B. M. W. Tsui, E. C. Frey, G. A. Johnson, and S. S. Berr, “Development of a 4-D digital mouse phantom for molecular imaging research,” Mol. Imaging Biol. 6(3), 149–159 (2004).
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S. Lee, G. Wolberg, and S. Y. Shin, “Scattered data interpolation with multilevel B-splines,” IEEE Trans. Vis. Comput. Graph. 3(3), 228–244 (1997).
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P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
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Y. Zhang, L. Chang, C. Ceritoglu, J. Skranes, T. Ernst, S. Mori, M. I. Miller, and K. Oishi, “A Bayesian approach to the creation of a study-customized neonatal brain atlas,” Neuroimage 101, 256–267 (2014).
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Sonoda, L. I.

D. Rueckert, L. I. Sonoda, C. Hayes, D. L. G. Hill, M. O. Leach, and D. J. Hawkes, “Nonrigid registration using free-form deformations: application to breast MR images,” IEEE Trans. Med. Imaging 18(8), 712–721 (1999).
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H. Dehghani, S. Srinivasan, B. W. Pogue, and A. Gibson, “Numerical modelling and image reconstruction in diffuse optical tomography,” Philos Trans A Math Phys Eng Sci 367(1900), 3073–3093 (2009).
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B. Dogdas, D. Stout, A. F. Chatziioannou, and R. M. Leahy, “Digimouse: a 3D whole body mouse atlas from CT and cryosection data,” Phys. Med. Biol. 52(3), 577–587 (2007).
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Tian, J.

Tichauer, K. M.

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P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
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Tsui, B. M. W.

W. P. Segars, B. M. W. Tsui, E. C. Frey, G. A. Johnson, and S. S. Berr, “Development of a 4-D digital mouse phantom for molecular imaging research,” Mol. Imaging Biol. 6(3), 149–159 (2004).
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P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
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F. Leblond, S. C. Davis, P. A. Valdés, and B. W. Pogue, “Pre-clinical whole-body fluorescence imaging: Review of instruments, methods and applications,” J. Photochem. Photobiol. B 98(1), 77–94 (2010).
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Van de Velde, J.

J. Van de Velde, J. Wouters, T. Vercauteren, W. De Gersem, E. Achten, W. De Neve, and T. Van Hoof, “Optimal number of atlases and label fusion for automatic multi-atlas-based brachial plexus contouring in radiotherapy treatment planning,” Radiat. Oncol. 11(1), 1 (2016).
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Van Hoof, T.

J. Van de Velde, J. Wouters, T. Vercauteren, W. De Gersem, E. Achten, W. De Neve, and T. Van Hoof, “Optimal number of atlases and label fusion for automatic multi-atlas-based brachial plexus contouring in radiotherapy treatment planning,” Radiat. Oncol. 11(1), 1 (2016).
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Vaquero, J. J.

J. F. P. J. Abascal, J. Aguirre, J. Chamorro-Servent, M. Schweiger, S. Arridge, J. Ripoll, J. J. Vaquero, and M. Desco, “Influence of absorption and scattering on the quantification of fluorescence diffuse optical tomography using normalized data,” J. Biomed. Opt. 17(3), 036013 (2012).
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Vercauteren, T.

J. Van de Velde, J. Wouters, T. Vercauteren, W. De Gersem, E. Achten, W. De Neve, and T. Van Hoof, “Optimal number of atlases and label fusion for automatic multi-atlas-based brachial plexus contouring in radiotherapy treatment planning,” Radiat. Oncol. 11(1), 1 (2016).
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Wan, W.

Wang, G.

Wang, L.

Wang, X.

Willner, M.

P. Mohajerani, A. Hipp, M. Willner, M. Marschner, M. Trajkovic-Arsic, X. Ma, N. C. Burton, U. Klemm, K. Radrich, V. Ermolayev, S. Tzoumas, J. T. Siveke, M. Bech, F. Pfeiffer, and V. Ntziachristos, “FMT-PCCT: hybrid fluorescence molecular tomography-x-ray phase-contrast CT imaging of mouse models,” IEEE Trans. Med. Imaging 33(7), 1434–1446 (2014).
[Crossref] [PubMed]

Wolberg, G.

S. Lee, G. Wolberg, and S. Y. Shin, “Scattered data interpolation with multilevel B-splines,” IEEE Trans. Vis. Comput. Graph. 3(3), 228–244 (1997).
[Crossref]

Wouters, J.

J. Van de Velde, J. Wouters, T. Vercauteren, W. De Gersem, E. Achten, W. De Neve, and T. Van Hoof, “Optimal number of atlases and label fusion for automatic multi-atlas-based brachial plexus contouring in radiotherapy treatment planning,” Radiat. Oncol. 11(1), 1 (2016).
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Wu, L.

Wu, X.

Xu, J.

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G. Zhang, F. Liu, H. Pu, W. He, J. Luo, and J. Bai, “A direct method with structural priors for imaging pharmacokinetic parameters in dynamic fluorescence molecular tomography,” IEEE Trans. Biomed. Eng. 61(3), 986–990 (2014).
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Figures (8)

Fig. 1
Fig. 1 The schematic of the proposed approach.
Fig. 2
Fig. 2 Two steps of the target atlas creation.
Fig. 3
Fig. 3 CT-analogous scanning mode for DOT measurement: (a) Sketch of the mouse model for simulation; (b) configuration of the source and detectors.
Fig. 4
Fig. 4 Volume registration: (a) Pseudo-color fused slices formed with the standard volume (in magenta) and the target volume (in green) before registration; (b) Pseudo-color fused slices formed with the registered standard volume (in magenta) and the standard volume (in green) after registration; (c) two-dimensional correlation coefficient of slices before registration and after registration.
Fig. 5
Fig. 5 Atlas registration: (a) Fused atlases before registration (b) Fused atlases after registration (c) Mean Euclidean distances of each organ before and after registration. For clearly showing the inner organs of atlases, muscle is not included.
Fig. 6
Fig. 6 Schematic of the CT-analogous scanning DOT setup.
Fig. 7
Fig. 7 Registration results: (a) Sagittal slice of the standard volume; (b)-(f) Pseudo-color fused sagittal slices of 5 mice after registration. The magenta parts illustrate the target volumes while the green parts illustrate the registered standard volumes.
Fig. 8
Fig. 8 Box-plot about the recovered (a) absorption coefficients and (b) reduced scattering coefficients of the main regions in KM mice.

Tables (2)

Tables Icon

Table 1 Simulated reconstruction of mouse organ optical properties with the atlas-registration.

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Table 2 Comparison of the recovered and published optical properties of mice

Equations (12)

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E(C,f)= i=1 N bs +1 j=1 N bt +1 c ij || b j (t) f( b i (s) )| | 2 +λT||Lf| | 2 +T i=1 N bs j=1 N bt c ij log c ij + T 0 j=1 N bt c N bs+1, j log c N bs+1, j + T 0 i=1 N bs c i, N bt +1 log c i, N bt +1
c ij ={ 1 T exp( ||( b j (t) f( b i (s) )| | 2 2T ) for i=1,2,..., N bs and j=1,2,..., N bt 1 T 0 exp( ||( b N bt +1 (t) f( b i (s) )| | 2 2 T 0 ) for i=1,2,..., N bs and j= N bt +1 1 T 0 exp( ||( b j (t) f( b N bs +1 (s) )| | 2 2 T 0 ) for i= N bs +1 and j=1,2,..., N bt
b i (r) = j=1 N bt c ij b j (t)
L (pre) =[ B (r) B (s) , S (r) S (s) ]
a i (pre) = a i (s) + d j (pre)
L (post) = P (pre) P (post)
a i (t) = a i (pre) + d j (post)
RF( μ (k) )= J (k) Δ μ (k) , μ (k+1) = μ (k) +Δ μ (k)
J ˜ (k) =[ J a (k) G J s (k) G]
G ij ={ 1ifi Ξ j 0otherwise
RF( μ ˜ (k) )= J ˜ (k) Δ μ ˜ (k) , μ ˜ (k+1) = μ ˜ (k) +Δ μ ˜ (k)
d (k) =( n=1 N k || ξ n (k) ζ n (k) || )/ N k

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