Abstract

Due to an ill-posed and underestimated characteristic of bioluminescence tomography (BLT) reconstruction, a priori anatomical information obtained from computed tomography (CT) or magnetic resonance imaging (MRI), is usually incorporated to improve the reconstruction accuracy. The organs need to be segmented, which is time-consuming and challenging, especially for the low-contrast CT images. In this paper, we present a BLT reconstruction method based on a statistical mouse atlas to improve the efficiency of heterogeneous model generation and the accuracy of target localization. The low-contrast CT image of the mouse was first registered to the statistical mouse atlas model with the constraints of mouse surface and high-contrast organs (bone and lung). Then the other organs, such as the liver and kidney, were determined automatically through the statistical mouse atlas model. The estimated organs were then discretized into tetrahedral meshes for BLT reconstruction. The linearized Bregman method was used to solve the sparse inverse problem of BLT by minimizing the regularization function (L1 norm plus L2 norm with smooth factor). Both numerical simulations and in vivo experiments were conducted, and the results demonstrate that even though the localization of the estimated organs may not be exactly accurate, the proposed method is feasible to reconstruct the bioluminescent source effectively and accurately with the estimated organs. This method would greatly benefit the bioluminescent light source localization for hybrid BLT/CT systems.

© 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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References

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  1. M. Keyaerts, V. Caveliers, and T. Lahoutte, “Bioluminescence imaging: looking beyond the light,” Trends Mol. Med. 18(3), 164–172 (2012).
    [Crossref] [PubMed]
  2. C. H. Qin, J. C. Feng, S. P. Zhu, X. B. Ma, J. H. Zhong, P. Wu, Z. Y. Jin, and J. Tian, “Recent advances in bioluminescence tomography: methodology and system as well as application,” Laser Photonics Rev. 8(1), 94–114 (2014).
    [Crossref]
  3. C. Darne, Y. Lu, and E. M. Sevick-Muraca, “Small animal fluorescence and bioluminescence tomography: a review of approaches, algorithms and technology update,” Phys. Med. Biol. 59(1), R1–R64 (2014).
    [Crossref] [PubMed]
  4. B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
    [Crossref] [PubMed]
  5. J. Shi, T. S. Udayakumar, K. Xu, N. Dogan, A. Pollack, and Y. Yang, “Bioluminescence tomography guided small-animal radiation therapy and tumor response assessment,” Int. J. Radiat. Oncol. Biol. Phys. S0360-3016(18)30182-2, epub ahead of print (2018).
    [PubMed]
  6. 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]
  7. G. Wang, W. Cong, K. Durairaj, X. Qian, H. Shen, P. Sinn, E. Hoffman, G. McLennan, and M. Henry, “In vivo mouse studies with bioluminescence tomography,” Opt. Express 14(17), 7801–7809 (2006).
    [Crossref] [PubMed]
  8. G. Wang, Y. Li, and M. Jiang, “Uniqueness theorems in bioluminescence tomography,” Med. Phys. 31(8), 2289–2299 (2004).
    [Crossref] [PubMed]
  9. J. Liu, Y. Wang, X. Qu, X. Li, X. Ma, R. Han, Z. Hu, X. Chen, D. Sun, R. Zhang, D. Chen, D. Chen, X. Chen, J. Liang, F. Cao, and J. Tian, “In vivo quantitative bioluminescence tomography using heterogeneous and homogeneous mouse models,” Opt. Express 18(12), 13102–13113 (2010).
    [Crossref] [PubMed]
  10. S. Yahyanejad, P. V. Granton, N. G. Lieuwes, L. Gilmour, L. Dubois, J. Theys, A. J. Chalmers, F. Verhaegen, and M. Vooijs, “Complementary use of bioluminescence imaging and contrast-enhanced micro-computed tomography in an orthotopic brain tumor model,” Mol. Imaging 13(1), 1–8 (2014).
    [PubMed]
  11. M. A. Naser, M. S. Patterson, and J. W. Wong, “Algorithm for localized adaptive diffuse optical tomography and its application in bioluminescence tomography,” Phys. Med. Biol. 59(8), 2089–2109 (2014).
    [Crossref] [PubMed]
  12. P. Wu, K. Liu, Q. Zhang, Z. Xue, Y. Li, N. Ning, X. Yang, X. Li, and J. Tian, “Detection of mouse liver cancer via a parallel iterative shrinkage method in hybrid optical/microcomputed tomography imaging,” J. Biomed. Opt. 17(12), 126012 (2012).
    [Crossref] [PubMed]
  13. H. Yan, Y. Lin, W. C. Barber, M. B. Unlu, and G. Gulsen, “A gantry-based tri-modality system for bioluminescence tomography,” Rev. Sci. Instrum. 83(4), 043708 (2012).
    [Crossref] [PubMed]
  14. A. D. Klose, B. J. Beattie, H. Dehghani, L. Vider, C. Le, V. Ponomarev, and R. Blasberg, “In vivo bioluminescence tomography with a blocking-off finite-difference SP3 method and MRI/CT coregistration,” Med. Phys. 37(1), 329–338 (2010).
    [Crossref] [PubMed]
  15. 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]
  16. 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]
  17. J. Zhang, D. Chen, J. Liang, H. Xue, J. Lei, Q. Wang, D. Chen, M. Meng, Z. Jin, and J. Tian, “Incorporating MRI structural information into bioluminescence tomography: system, heterogeneous reconstruction and in vivo quantification,” Biomed. Opt. Express 5(6), 1861–1876 (2014).
    [Crossref] [PubMed]
  18. H. Park, P. H. Bland, and C. R. Meyer, “Construction of an abdominal probabilistic atlas and its application in segmentation,” IEEE Trans. Med. Imaging 22(4), 483–492 (2003).
    [Crossref] [PubMed]
  19. C. Platero and M. C. Tobar, “A multi-atlas segmentation using graph cuts with applications to liver segmentation in CT scans,” Comput. Math. Methods Med. 2014, 182909 (2014).
    [Crossref] [PubMed]
  20. M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
    [Crossref] [PubMed]
  21. A. J. Chaudhari, A. A. Joshi, F. Darvas, and R. M. Leahy, “A method for atlas-based volumetric registration with surface constraints for optical bioluminescence tomography in small animal imaging,” Proc. SPIE 6510, 651024 (2007).
    [Crossref]
  22. M. Baiker, M. Staring, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Automated registration of whole-body follow-up MicroCT data of mice,” Med Image Comput Comput Assist Interv 14(Pt 2), 516–523 (2011).
    [PubMed]
  23. D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, H. Green, M. C. Gregoire, and O. Salvado, “Mouse whole-body organ mapping by non-rigid registration approach,” Proc. SPIE 7965, 79650E (2011).
    [Crossref]
  24. W. P. Segars, B. M. 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]
  25. 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]
  26. W. Wan, Y. Wang, J. Qi, L. Liu, W. Ma, J. Li, L. Zhang, Z. Zhou, H. Zhao, and F. Gao, “Region-based diffuse optical tomography with registered atlas: in vivo acquisition of mouse optical properties,” Biomed. Opt. Express 7(12), 5066–5080 (2016).
    [Crossref] [PubMed]
  27. S. Ren, H. Hu, G. Li, X. Cao, S. Zhu, X. Chen, and J. Liang, “Multi-atlas registration and adaptive hexahedral voxel discretization for fast bioluminescence tomography,” Biomed. Opt. Express 7(4), 1549–1560 (2016).
    [Crossref] [PubMed]
  28. H. Wang, D. B. Stout, and A. F. Chatziioannou, “Estimation of mouse organ locations through registration of a statistical mouse atlas with micro-CT images,” IEEE Trans. Med. Imaging 31(1), 88–102 (2012).
    [Crossref] [PubMed]
  29. H. Wang, D. B. Stout, and A. F. Chatziioannou, “A deformable atlas of the laboratory mouse,” Mol. Imaging Biol. 17(1), 18–28 (2015).
    [Crossref] [PubMed]
  30. G. Wang, W. X. Cong, Q. S. Yang, Q. Pian, S. P. Zhu, J. M. Liang, M. Barroso, and X. Intes, “Innovation and fusion of X-ray and optical tomography for mouse studies of breast cancer,” Proc. SPIE 9967, 99671R (2016).
    [Crossref]
  31. A. D. Klose and E. W. Larsen, “Light transport in biological tissue based on the simplified spherical harmonics equations,” J. Comput. Phys. 220(1), 441–470 (2006).
    [Crossref]
  32. K. Liu, Y. Lu, J. Tian, C. Qin, X. Yang, S. Zhu, X. Yang, Q. Gao, and D. Han, “Evaluation of the simplified spherical harmonics approximation in bioluminescence tomography through heterogeneous mouse models,” Opt. Express 18(20), 20988–21002 (2010).
    [Crossref] [PubMed]
  33. C. Kuo, O. Coquoz, T. L. Troy, H. Xu, and B. W. Rice, “Three-dimensional reconstruction of in vivo bioluminescent sources based on multispectral imaging,” J. Biomed. Opt. 12(2), 024007 (2007).
    [Crossref] [PubMed]
  34. H. Dehghani, S. C. Davis, S. Jiang, B. W. Pogue, K. D. Paulsen, and M. S. Patterson, “Spectrally resolved bioluminescence optical tomography,” Opt. Lett. 31(3), 365–367 (2006).
    [Crossref] [PubMed]
  35. M. Jermyn, H. Ghadyani, M. A. Mastanduno, W. Turner, S. C. Davis, H. Dehghani, and B. W. Pogue, “Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography,” J. Biomed. Opt. 18(8), 086007 (2013).
    [Crossref] [PubMed]
  36. H. Dehghani, M. E. Eames, P. K. Yalavarthy, S. C. Davis, S. Srinivasan, C. M. Carpenter, B. W. Pogue, and K. D. Paulsen, “Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction,” Commun. Numer. Methods Eng. 25(6), 711–732 (2008).
    [Crossref] [PubMed]
  37. W. T. Yin, “Analysis and generalizations of the linearized Bregman method,” SIAM J. Imaging Sci. 3(4), 856–877 (2010).
    [Crossref]
  38. S. L. Jacques, “Optical properties of biological tissues: a review,” Phys. Med. Biol. 58(11), R37–R61 (2013).
    [Crossref] [PubMed]
  39. 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]
  40. S. Zhang, K. Wang, H. Liu, C. Leng, Y. Gao, and J. Tian, “Reconstruction method for in vivo bioluminescence tomography based on the split Bregman iterative and surrogate functions,” Mol. Imaging Biol. 19(2), 245–255 (2017).
    [Crossref] [PubMed]
  41. C. Leng, D. Yu, S. Zhang, Y. An, and Y. Hu, “Reconstruction method for optical tomography based on the linearized Bregman iteration with sparse regularization,” Comput. Math. Methods Med. 2015, 304191 (2015).
    [Crossref] [PubMed]
  42. H. Gao and H. Zhao, “Multilevel bioluminescence tomography based on radiative transfer equation Part 1: l1 regularization,” Opt. Express 18(3), 1854–1871 (2010).
    [Crossref] [PubMed]
  43. X. He, J. Liang, X. Wang, J. Yu, X. Qu, X. Wang, Y. Hou, D. Chen, F. Liu, and J. Tian, “Sparse reconstruction for quantitative bioluminescence tomography based on the incomplete variables truncated conjugate gradient method,” Opt. Express 18(24), 24825–24841 (2010).
    [Crossref] [PubMed]
  44. J. Shi, B. Zhang, F. Liu, J. Luo, and J. Bai, “Efficient L1 regularization-based reconstruction for fluorescent molecular tomography using restarted nonlinear conjugate gradient,” Opt. Lett. 38(18), 3696–3699 (2013).
    [Crossref] [PubMed]
  45. Q. Zhang, X. Chen, X. Qu, J. Liang, and J. Tian, “Comparative studies of l(p)-regularization-based reconstruction algorithms for bioluminescence tomography,” Biomed. Opt. Express 3(11), 2916–2936 (2012).
    [Crossref] [PubMed]
  46. S. Jiang, J. Liu, Y. An, G. Zhang, J. Ye, Y. Mao, K. He, C. Chi, and J. Tian, “Novel l 2,1-norm optimization method for fluorescence molecular tomography reconstruction,” Biomed. Opt. Express 7(6), 2342–2359 (2016).
    [Crossref] [PubMed]
  47. S. M. Hejazi, S. Sarkar, and Z. Darezereshki, “Fast multislice fluorescence molecular tomography using sparsity-inducing regularization,” J. Biomed. Opt. 21(2), 026012 (2016).
    [Crossref] [PubMed]

2017 (1)

S. Zhang, K. Wang, H. Liu, C. Leng, Y. Gao, and J. Tian, “Reconstruction method for in vivo bioluminescence tomography based on the split Bregman iterative and surrogate functions,” Mol. Imaging Biol. 19(2), 245–255 (2017).
[Crossref] [PubMed]

2016 (6)

S. Jiang, J. Liu, Y. An, G. Zhang, J. Ye, Y. Mao, K. He, C. Chi, and J. Tian, “Novel l 2,1-norm optimization method for fluorescence molecular tomography reconstruction,” Biomed. Opt. Express 7(6), 2342–2359 (2016).
[Crossref] [PubMed]

S. M. Hejazi, S. Sarkar, and Z. Darezereshki, “Fast multislice fluorescence molecular tomography using sparsity-inducing regularization,” J. Biomed. Opt. 21(2), 026012 (2016).
[Crossref] [PubMed]

B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
[Crossref] [PubMed]

W. Wan, Y. Wang, J. Qi, L. Liu, W. Ma, J. Li, L. Zhang, Z. Zhou, H. Zhao, and F. Gao, “Region-based diffuse optical tomography with registered atlas: in vivo acquisition of mouse optical properties,” Biomed. Opt. Express 7(12), 5066–5080 (2016).
[Crossref] [PubMed]

S. Ren, H. Hu, G. Li, X. Cao, S. Zhu, X. Chen, and J. Liang, “Multi-atlas registration and adaptive hexahedral voxel discretization for fast bioluminescence tomography,” Biomed. Opt. Express 7(4), 1549–1560 (2016).
[Crossref] [PubMed]

G. Wang, W. X. Cong, Q. S. Yang, Q. Pian, S. P. Zhu, J. M. Liang, M. Barroso, and X. Intes, “Innovation and fusion of X-ray and optical tomography for mouse studies of breast cancer,” Proc. SPIE 9967, 99671R (2016).
[Crossref]

2015 (2)

H. Wang, D. B. Stout, and A. F. Chatziioannou, “A deformable atlas of the laboratory mouse,” Mol. Imaging Biol. 17(1), 18–28 (2015).
[Crossref] [PubMed]

C. Leng, D. Yu, S. Zhang, Y. An, and Y. Hu, “Reconstruction method for optical tomography based on the linearized Bregman iteration with sparse regularization,” Comput. Math. Methods Med. 2015, 304191 (2015).
[Crossref] [PubMed]

2014 (7)

C. H. Qin, J. C. Feng, S. P. Zhu, X. B. Ma, J. H. Zhong, P. Wu, Z. Y. Jin, and J. Tian, “Recent advances in bioluminescence tomography: methodology and system as well as application,” Laser Photonics Rev. 8(1), 94–114 (2014).
[Crossref]

C. Darne, Y. Lu, and E. M. Sevick-Muraca, “Small animal fluorescence and bioluminescence tomography: a review of approaches, algorithms and technology update,” Phys. Med. Biol. 59(1), R1–R64 (2014).
[Crossref] [PubMed]

S. Yahyanejad, P. V. Granton, N. G. Lieuwes, L. Gilmour, L. Dubois, J. Theys, A. J. Chalmers, F. Verhaegen, and M. Vooijs, “Complementary use of bioluminescence imaging and contrast-enhanced micro-computed tomography in an orthotopic brain tumor model,” Mol. Imaging 13(1), 1–8 (2014).
[PubMed]

M. A. Naser, M. S. Patterson, and J. W. Wong, “Algorithm for localized adaptive diffuse optical tomography and its application in bioluminescence tomography,” Phys. Med. Biol. 59(8), 2089–2109 (2014).
[Crossref] [PubMed]

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]

J. Zhang, D. Chen, J. Liang, H. Xue, J. Lei, Q. Wang, D. Chen, M. Meng, Z. Jin, and J. Tian, “Incorporating MRI structural information into bioluminescence tomography: system, heterogeneous reconstruction and in vivo quantification,” Biomed. Opt. Express 5(6), 1861–1876 (2014).
[Crossref] [PubMed]

C. Platero and M. C. Tobar, “A multi-atlas segmentation using graph cuts with applications to liver segmentation in CT scans,” Comput. Math. Methods Med. 2014, 182909 (2014).
[Crossref] [PubMed]

2013 (3)

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

M. Jermyn, H. Ghadyani, M. A. Mastanduno, W. Turner, S. C. Davis, H. Dehghani, and B. W. Pogue, “Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography,” J. Biomed. Opt. 18(8), 086007 (2013).
[Crossref] [PubMed]

J. Shi, B. Zhang, F. Liu, J. Luo, and J. Bai, “Efficient L1 regularization-based reconstruction for fluorescent molecular tomography using restarted nonlinear conjugate gradient,” Opt. Lett. 38(18), 3696–3699 (2013).
[Crossref] [PubMed]

2012 (6)

Q. Zhang, X. Chen, X. Qu, J. Liang, and J. Tian, “Comparative studies of l(p)-regularization-based reconstruction algorithms for bioluminescence tomography,” Biomed. Opt. Express 3(11), 2916–2936 (2012).
[Crossref] [PubMed]

H. Wang, D. B. Stout, and A. F. Chatziioannou, “Estimation of mouse organ locations through registration of a statistical mouse atlas with micro-CT images,” IEEE Trans. Med. Imaging 31(1), 88–102 (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]

P. Wu, K. Liu, Q. Zhang, Z. Xue, Y. Li, N. Ning, X. Yang, X. Li, and J. Tian, “Detection of mouse liver cancer via a parallel iterative shrinkage method in hybrid optical/microcomputed tomography imaging,” J. Biomed. Opt. 17(12), 126012 (2012).
[Crossref] [PubMed]

H. Yan, Y. Lin, W. C. Barber, M. B. Unlu, and G. Gulsen, “A gantry-based tri-modality system for bioluminescence tomography,” Rev. Sci. Instrum. 83(4), 043708 (2012).
[Crossref] [PubMed]

M. Keyaerts, V. Caveliers, and T. Lahoutte, “Bioluminescence imaging: looking beyond the light,” Trends Mol. Med. 18(3), 164–172 (2012).
[Crossref] [PubMed]

2011 (2)

M. Baiker, M. Staring, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Automated registration of whole-body follow-up MicroCT data of mice,” Med Image Comput Comput Assist Interv 14(Pt 2), 516–523 (2011).
[PubMed]

D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, H. Green, M. C. Gregoire, and O. Salvado, “Mouse whole-body organ mapping by non-rigid registration approach,” Proc. SPIE 7965, 79650E (2011).
[Crossref]

2010 (7)

K. Liu, Y. Lu, J. Tian, C. Qin, X. Yang, S. Zhu, X. Yang, Q. Gao, and D. Han, “Evaluation of the simplified spherical harmonics approximation in bioluminescence tomography through heterogeneous mouse models,” Opt. Express 18(20), 20988–21002 (2010).
[Crossref] [PubMed]

W. T. Yin, “Analysis and generalizations of the linearized Bregman method,” SIAM J. Imaging Sci. 3(4), 856–877 (2010).
[Crossref]

J. Liu, Y. Wang, X. Qu, X. Li, X. Ma, R. Han, Z. Hu, X. Chen, D. Sun, R. Zhang, D. Chen, D. Chen, X. Chen, J. Liang, F. Cao, and J. Tian, “In vivo quantitative bioluminescence tomography using heterogeneous and homogeneous mouse models,” Opt. Express 18(12), 13102–13113 (2010).
[Crossref] [PubMed]

A. D. Klose, B. J. Beattie, H. Dehghani, L. Vider, C. Le, V. Ponomarev, and R. Blasberg, “In vivo bioluminescence tomography with a blocking-off finite-difference SP3 method and MRI/CT coregistration,” Med. Phys. 37(1), 329–338 (2010).
[Crossref] [PubMed]

M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
[Crossref] [PubMed]

H. Gao and H. Zhao, “Multilevel bioluminescence tomography based on radiative transfer equation Part 1: l1 regularization,” Opt. Express 18(3), 1854–1871 (2010).
[Crossref] [PubMed]

X. He, J. Liang, X. Wang, J. Yu, X. Qu, X. Wang, Y. Hou, D. Chen, F. Liu, and J. Tian, “Sparse reconstruction for quantitative bioluminescence tomography based on the incomplete variables truncated conjugate gradient method,” Opt. Express 18(24), 24825–24841 (2010).
[Crossref] [PubMed]

2008 (1)

H. Dehghani, M. E. Eames, P. K. Yalavarthy, S. C. Davis, S. Srinivasan, C. M. Carpenter, B. W. Pogue, and K. D. Paulsen, “Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction,” Commun. Numer. Methods Eng. 25(6), 711–732 (2008).
[Crossref] [PubMed]

2007 (3)

C. Kuo, O. Coquoz, T. L. Troy, H. Xu, and B. W. Rice, “Three-dimensional reconstruction of in vivo bioluminescent sources based on multispectral imaging,” J. Biomed. Opt. 12(2), 024007 (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]

A. J. Chaudhari, A. A. Joshi, F. Darvas, and R. M. Leahy, “A method for atlas-based volumetric registration with surface constraints for optical bioluminescence tomography in small animal imaging,” Proc. SPIE 6510, 651024 (2007).
[Crossref]

2006 (3)

2005 (2)

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]

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]

2004 (2)

G. Wang, Y. Li, and M. Jiang, “Uniqueness theorems in bioluminescence tomography,” Med. Phys. 31(8), 2289–2299 (2004).
[Crossref] [PubMed]

W. P. Segars, B. M. 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. Park, P. H. Bland, and C. R. Meyer, “Construction of an abdominal probabilistic atlas and its application in segmentation,” IEEE Trans. Med. Imaging 22(4), 483–492 (2003).
[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]

An, Y.

S. Jiang, J. Liu, Y. An, G. Zhang, J. Ye, Y. Mao, K. He, C. Chi, and J. Tian, “Novel l 2,1-norm optimization method for fluorescence molecular tomography reconstruction,” Biomed. Opt. Express 7(6), 2342–2359 (2016).
[Crossref] [PubMed]

C. Leng, D. Yu, S. Zhang, Y. An, and Y. Hu, “Reconstruction method for optical tomography based on the linearized Bregman iteration with sparse regularization,” Comput. Math. Methods Med. 2015, 304191 (2015).
[Crossref] [PubMed]

Bai, J.

Baiker, M.

M. Baiker, M. Staring, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Automated registration of whole-body follow-up MicroCT data of mice,” Med Image Comput Comput Assist Interv 14(Pt 2), 516–523 (2011).
[PubMed]

M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
[Crossref] [PubMed]

Barber, W. C.

H. Yan, Y. Lin, W. C. Barber, M. B. Unlu, and G. Gulsen, “A gantry-based tri-modality system for bioluminescence tomography,” Rev. Sci. Instrum. 83(4), 043708 (2012).
[Crossref] [PubMed]

Barroso, M.

G. Wang, W. X. Cong, Q. S. Yang, Q. Pian, S. P. Zhu, J. M. Liang, M. Barroso, and X. Intes, “Innovation and fusion of X-ray and optical tomography for mouse studies of breast cancer,” Proc. SPIE 9967, 99671R (2016).
[Crossref]

Beattie, B. J.

A. D. Klose, B. J. Beattie, H. Dehghani, L. Vider, C. Le, V. Ponomarev, and R. Blasberg, “In vivo bioluminescence tomography with a blocking-off finite-difference SP3 method and MRI/CT coregistration,” Med. Phys. 37(1), 329–338 (2010).
[Crossref] [PubMed]

Berghofer, P.

D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, H. Green, M. C. Gregoire, and O. Salvado, “Mouse whole-body organ mapping by non-rigid registration approach,” Proc. SPIE 7965, 79650E (2011).
[Crossref]

Berr, S. S.

W. P. Segars, B. M. 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.

Bland, P. H.

H. Park, P. H. Bland, and C. R. Meyer, “Construction of an abdominal probabilistic atlas and its application in segmentation,” IEEE Trans. Med. Imaging 22(4), 483–492 (2003).
[Crossref] [PubMed]

Blasberg, R.

A. D. Klose, B. J. Beattie, H. Dehghani, L. Vider, C. Le, V. Ponomarev, and R. Blasberg, “In vivo bioluminescence tomography with a blocking-off finite-difference SP3 method and MRI/CT coregistration,” Med. Phys. 37(1), 329–338 (2010).
[Crossref] [PubMed]

Bourgeat, P.

D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, H. Green, M. C. Gregoire, and O. Salvado, “Mouse whole-body organ mapping by non-rigid registration approach,” Proc. SPIE 7965, 79650E (2011).
[Crossref]

Cao, F.

Cao, X.

Carpenter, C. M.

H. Dehghani, M. E. Eames, P. K. Yalavarthy, S. C. Davis, S. Srinivasan, C. M. Carpenter, B. W. Pogue, and K. D. Paulsen, “Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction,” Commun. Numer. Methods Eng. 25(6), 711–732 (2008).
[Crossref] [PubMed]

Caveliers, V.

M. Keyaerts, V. Caveliers, and T. Lahoutte, “Bioluminescence imaging: looking beyond the light,” Trends Mol. Med. 18(3), 164–172 (2012).
[Crossref] [PubMed]

Chalmers, A. J.

S. Yahyanejad, P. V. Granton, N. G. Lieuwes, L. Gilmour, L. Dubois, J. Theys, A. J. Chalmers, F. Verhaegen, and M. Vooijs, “Complementary use of bioluminescence imaging and contrast-enhanced micro-computed tomography in an orthotopic brain tumor model,” Mol. Imaging 13(1), 1–8 (2014).
[PubMed]

Chatziioannou, A. F.

H. Wang, D. B. Stout, and A. F. Chatziioannou, “A deformable atlas of the laboratory mouse,” Mol. Imaging Biol. 17(1), 18–28 (2015).
[Crossref] [PubMed]

H. Wang, D. B. Stout, and A. F. Chatziioannou, “Estimation of mouse organ locations through registration of a statistical mouse atlas with micro-CT images,” IEEE Trans. Med. Imaging 31(1), 88–102 (2012).
[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]

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]

Chaudhari, A. J.

A. J. Chaudhari, A. A. Joshi, F. Darvas, and R. M. Leahy, “A method for atlas-based volumetric registration with surface constraints for optical bioluminescence tomography in small animal imaging,” Proc. SPIE 6510, 651024 (2007).
[Crossref]

Chen, D.

J. Zhang, D. Chen, J. Liang, H. Xue, J. Lei, Q. Wang, D. Chen, M. Meng, Z. Jin, and J. Tian, “Incorporating MRI structural information into bioluminescence tomography: system, heterogeneous reconstruction and in vivo quantification,” Biomed. Opt. Express 5(6), 1861–1876 (2014).
[Crossref] [PubMed]

J. Zhang, D. Chen, J. Liang, H. Xue, J. Lei, Q. Wang, D. Chen, M. Meng, Z. Jin, and J. Tian, “Incorporating MRI structural information into bioluminescence tomography: system, heterogeneous reconstruction and in vivo quantification,” Biomed. Opt. Express 5(6), 1861–1876 (2014).
[Crossref] [PubMed]

J. Liu, Y. Wang, X. Qu, X. Li, X. Ma, R. Han, Z. Hu, X. Chen, D. Sun, R. Zhang, D. Chen, D. Chen, X. Chen, J. Liang, F. Cao, and J. Tian, “In vivo quantitative bioluminescence tomography using heterogeneous and homogeneous mouse models,” Opt. Express 18(12), 13102–13113 (2010).
[Crossref] [PubMed]

J. Liu, Y. Wang, X. Qu, X. Li, X. Ma, R. Han, Z. Hu, X. Chen, D. Sun, R. Zhang, D. Chen, D. Chen, X. Chen, J. Liang, F. Cao, and J. Tian, “In vivo quantitative bioluminescence tomography using heterogeneous and homogeneous mouse models,” Opt. Express 18(12), 13102–13113 (2010).
[Crossref] [PubMed]

X. He, J. Liang, X. Wang, J. Yu, X. Qu, X. Wang, Y. Hou, D. Chen, F. Liu, and J. Tian, “Sparse reconstruction for quantitative bioluminescence tomography based on the incomplete variables truncated conjugate gradient method,” Opt. Express 18(24), 24825–24841 (2010).
[Crossref] [PubMed]

Chen, X.

Chi, C.

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.

Cong, W. X.

G. Wang, W. X. Cong, Q. S. Yang, Q. Pian, S. P. Zhu, J. M. Liang, M. Barroso, and X. Intes, “Innovation and fusion of X-ray and optical tomography for mouse studies of breast cancer,” Proc. SPIE 9967, 99671R (2016).
[Crossref]

Coquoz, O.

C. Kuo, O. Coquoz, T. L. Troy, H. Xu, and B. W. Rice, “Three-dimensional reconstruction of in vivo bioluminescent sources based on multispectral imaging,” J. Biomed. Opt. 12(2), 024007 (2007).
[Crossref] [PubMed]

Darezereshki, Z.

S. M. Hejazi, S. Sarkar, and Z. Darezereshki, “Fast multislice fluorescence molecular tomography using sparsity-inducing regularization,” J. Biomed. Opt. 21(2), 026012 (2016).
[Crossref] [PubMed]

Darne, C.

C. Darne, Y. Lu, and E. M. Sevick-Muraca, “Small animal fluorescence and bioluminescence tomography: a review of approaches, algorithms and technology update,” Phys. Med. Biol. 59(1), R1–R64 (2014).
[Crossref] [PubMed]

Darvas, F.

A. J. Chaudhari, A. A. Joshi, F. Darvas, and R. M. Leahy, “A method for atlas-based volumetric registration with surface constraints for optical bioluminescence tomography in small animal imaging,” Proc. SPIE 6510, 651024 (2007).
[Crossref]

Davis, S. C.

M. Jermyn, H. Ghadyani, M. A. Mastanduno, W. Turner, S. C. Davis, H. Dehghani, and B. W. Pogue, “Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography,” J. Biomed. Opt. 18(8), 086007 (2013).
[Crossref] [PubMed]

H. Dehghani, M. E. Eames, P. K. Yalavarthy, S. C. Davis, S. Srinivasan, C. M. Carpenter, B. W. Pogue, and K. D. Paulsen, “Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction,” Commun. Numer. Methods Eng. 25(6), 711–732 (2008).
[Crossref] [PubMed]

H. Dehghani, S. C. Davis, S. Jiang, B. W. Pogue, K. D. Paulsen, and M. S. Patterson, “Spectrally resolved bioluminescence optical tomography,” Opt. Lett. 31(3), 365–367 (2006).
[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]

Dehghani, H.

M. Jermyn, H. Ghadyani, M. A. Mastanduno, W. Turner, S. C. Davis, H. Dehghani, and B. W. Pogue, “Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography,” J. Biomed. Opt. 18(8), 086007 (2013).
[Crossref] [PubMed]

A. D. Klose, B. J. Beattie, H. Dehghani, L. Vider, C. Le, V. Ponomarev, and R. Blasberg, “In vivo bioluminescence tomography with a blocking-off finite-difference SP3 method and MRI/CT coregistration,” Med. Phys. 37(1), 329–338 (2010).
[Crossref] [PubMed]

H. Dehghani, M. E. Eames, P. K. Yalavarthy, S. C. Davis, S. Srinivasan, C. M. Carpenter, B. W. Pogue, and K. D. Paulsen, “Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction,” Commun. Numer. Methods Eng. 25(6), 711–732 (2008).
[Crossref] [PubMed]

H. Dehghani, S. C. Davis, S. Jiang, B. W. Pogue, K. D. Paulsen, and M. S. Patterson, “Spectrally resolved bioluminescence optical tomography,” Opt. Lett. 31(3), 365–367 (2006).
[Crossref] [PubMed]

Dijkstra, J.

M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
[Crossref] [PubMed]

Dogan, N.

J. Shi, T. S. Udayakumar, K. Xu, N. Dogan, A. Pollack, and Y. Yang, “Bioluminescence tomography guided small-animal radiation therapy and tumor response assessment,” Int. J. Radiat. Oncol. Biol. Phys. S0360-3016(18)30182-2, epub ahead of print (2018).
[PubMed]

Dogdas, B.

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]

Dubois, L.

S. Yahyanejad, P. V. Granton, N. G. Lieuwes, L. Gilmour, L. Dubois, J. Theys, A. J. Chalmers, F. Verhaegen, and M. Vooijs, “Complementary use of bioluminescence imaging and contrast-enhanced micro-computed tomography in an orthotopic brain tumor model,” Mol. Imaging 13(1), 1–8 (2014).
[PubMed]

Durairaj, K.

Eames, M. E.

H. Dehghani, M. E. Eames, P. K. Yalavarthy, S. C. Davis, S. Srinivasan, C. M. Carpenter, B. W. Pogue, and K. D. Paulsen, “Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction,” Commun. Numer. Methods Eng. 25(6), 711–732 (2008).
[Crossref] [PubMed]

Ermolayev, V.

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]

Eslami, S.

B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
[Crossref] [PubMed]

Feng, J. C.

C. H. Qin, J. C. Feng, S. P. Zhu, X. B. Ma, J. H. Zhong, P. Wu, Z. Y. Jin, and J. Tian, “Recent advances in bioluminescence tomography: methodology and system as well as application,” Laser Photonics Rev. 8(1), 94–114 (2014).
[Crossref]

Frey, E. C.

W. P. Segars, B. M. 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]

Gao, F.

Gao, H.

Gao, Q.

Gao, Y.

S. Zhang, K. Wang, H. Liu, C. Leng, Y. Gao, and J. Tian, “Reconstruction method for in vivo bioluminescence tomography based on the split Bregman iterative and surrogate functions,” Mol. Imaging Biol. 19(2), 245–255 (2017).
[Crossref] [PubMed]

Ghadyani, H.

M. Jermyn, H. Ghadyani, M. A. Mastanduno, W. Turner, S. C. Davis, H. Dehghani, and B. W. Pogue, “Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography,” J. Biomed. Opt. 18(8), 086007 (2013).
[Crossref] [PubMed]

Gilmour, L.

S. Yahyanejad, P. V. Granton, N. G. Lieuwes, L. Gilmour, L. Dubois, J. Theys, A. J. Chalmers, F. Verhaegen, and M. Vooijs, “Complementary use of bioluminescence imaging and contrast-enhanced micro-computed tomography in an orthotopic brain tumor model,” Mol. Imaging 13(1), 1–8 (2014).
[PubMed]

Granton, P. V.

S. Yahyanejad, P. V. Granton, N. G. Lieuwes, L. Gilmour, L. Dubois, J. Theys, A. J. Chalmers, F. Verhaegen, and M. Vooijs, “Complementary use of bioluminescence imaging and contrast-enhanced micro-computed tomography in an orthotopic brain tumor model,” Mol. Imaging 13(1), 1–8 (2014).
[PubMed]

Green, H.

D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, H. Green, M. C. Gregoire, and O. Salvado, “Mouse whole-body organ mapping by non-rigid registration approach,” Proc. SPIE 7965, 79650E (2011).
[Crossref]

Gregoire, M. C.

D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, H. Green, M. C. Gregoire, and O. Salvado, “Mouse whole-body organ mapping by non-rigid registration approach,” Proc. SPIE 7965, 79650E (2011).
[Crossref]

Gulsen, G.

H. Yan, Y. Lin, W. C. Barber, M. B. Unlu, and G. Gulsen, “A gantry-based tri-modality system for bioluminescence tomography,” Rev. Sci. Instrum. 83(4), 043708 (2012).
[Crossref] [PubMed]

Han, D.

Han, R.

He, K.

He, X.

Hejazi, S. M.

S. M. Hejazi, S. Sarkar, and Z. Darezereshki, “Fast multislice fluorescence molecular tomography using sparsity-inducing regularization,” J. Biomed. Opt. 21(2), 026012 (2016).
[Crossref] [PubMed]

Henning, T. D.

M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
[Crossref] [PubMed]

Henry, M.

Herzog, E.

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]

Hoffman, E.

Hou, Y.

Hu, H.

Hu, Y.

C. Leng, D. Yu, S. Zhang, Y. An, and Y. Hu, “Reconstruction method for optical tomography based on the linearized Bregman iteration with sparse regularization,” Comput. Math. Methods Med. 2015, 304191 (2015).
[Crossref] [PubMed]

Hu, Z.

Intes, X.

G. Wang, W. X. Cong, Q. S. Yang, Q. Pian, S. P. Zhu, J. M. Liang, M. Barroso, and X. Intes, “Innovation and fusion of X-ray and optical tomography for mouse studies of breast cancer,” Proc. SPIE 9967, 99671R (2016).
[Crossref]

Iordachita, I.

B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
[Crossref] [PubMed]

Jacques, S. L.

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

Jermyn, M.

M. Jermyn, H. Ghadyani, M. A. Mastanduno, W. Turner, S. C. Davis, H. Dehghani, and B. W. Pogue, “Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography,” J. Biomed. Opt. 18(8), 086007 (2013).
[Crossref] [PubMed]

Jiang, M.

Jiang, S.

Jin, Z.

Jin, Z. Y.

C. H. Qin, J. C. Feng, S. P. Zhu, X. B. Ma, J. H. Zhong, P. Wu, Z. Y. Jin, and J. Tian, “Recent advances in bioluminescence tomography: methodology and system as well as application,” Laser Photonics Rev. 8(1), 94–114 (2014).
[Crossref]

Johnson, G. A.

W. P. Segars, B. M. 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]

Joshi, A. A.

A. J. Chaudhari, A. A. Joshi, F. Darvas, and R. M. Leahy, “A method for atlas-based volumetric registration with surface constraints for optical bioluminescence tomography in small animal imaging,” Proc. SPIE 6510, 651024 (2007).
[Crossref]

Kaijzel, E. L.

M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
[Crossref] [PubMed]

Keyaerts, M.

M. Keyaerts, V. Caveliers, and T. Lahoutte, “Bioluminescence imaging: looking beyond the light,” Trends Mol. Med. 18(3), 164–172 (2012).
[Crossref] [PubMed]

Klose, A. D.

A. D. Klose, B. J. Beattie, H. Dehghani, L. Vider, C. Le, V. Ponomarev, and R. Blasberg, “In vivo bioluminescence tomography with a blocking-off finite-difference SP3 method and MRI/CT coregistration,” Med. Phys. 37(1), 329–338 (2010).
[Crossref] [PubMed]

A. D. Klose and E. W. Larsen, “Light transport in biological tissue based on the simplified spherical harmonics equations,” J. Comput. Phys. 220(1), 441–470 (2006).
[Crossref]

Kumar, D.

Kuo, C.

C. Kuo, O. Coquoz, T. L. Troy, H. Xu, and B. W. Rice, “Three-dimensional reconstruction of in vivo bioluminescent sources based on multispectral imaging,” J. Biomed. Opt. 12(2), 024007 (2007).
[Crossref] [PubMed]

Lahoutte, T.

M. Keyaerts, V. Caveliers, and T. Lahoutte, “Bioluminescence imaging: looking beyond the light,” Trends Mol. Med. 18(3), 164–172 (2012).
[Crossref] [PubMed]

Larsen, E. W.

A. D. Klose and E. W. Larsen, “Light transport in biological tissue based on the simplified spherical harmonics equations,” J. Comput. Phys. 220(1), 441–470 (2006).
[Crossref]

Le, C.

A. D. Klose, B. J. Beattie, H. Dehghani, L. Vider, C. Le, V. Ponomarev, and R. Blasberg, “In vivo bioluminescence tomography with a blocking-off finite-difference SP3 method and MRI/CT coregistration,” Med. Phys. 37(1), 329–338 (2010).
[Crossref] [PubMed]

Leahy, R. M.

A. J. Chaudhari, A. A. Joshi, F. Darvas, and R. M. Leahy, “A method for atlas-based volumetric registration with surface constraints for optical bioluminescence tomography in small animal imaging,” Proc. SPIE 6510, 651024 (2007).
[Crossref]

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]

Lei, J.

Lelieveldt, B. P.

M. Baiker, M. Staring, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Automated registration of whole-body follow-up MicroCT data of mice,” Med Image Comput Comput Assist Interv 14(Pt 2), 516–523 (2011).
[PubMed]

M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
[Crossref] [PubMed]

Leng, C.

S. Zhang, K. Wang, H. Liu, C. Leng, Y. Gao, and J. Tian, “Reconstruction method for in vivo bioluminescence tomography based on the split Bregman iterative and surrogate functions,” Mol. Imaging Biol. 19(2), 245–255 (2017).
[Crossref] [PubMed]

C. Leng, D. Yu, S. Zhang, Y. An, and Y. Hu, “Reconstruction method for optical tomography based on the linearized Bregman iteration with sparse regularization,” Comput. Math. Methods Med. 2015, 304191 (2015).
[Crossref] [PubMed]

Lesage, F.

Li, B.

Li, G.

Li, J.

Li, X.

P. Wu, K. Liu, Q. Zhang, Z. Xue, Y. Li, N. Ning, X. Yang, X. Li, and J. Tian, “Detection of mouse liver cancer via a parallel iterative shrinkage method in hybrid optical/microcomputed tomography imaging,” J. Biomed. Opt. 17(12), 126012 (2012).
[Crossref] [PubMed]

J. Liu, Y. Wang, X. Qu, X. Li, X. Ma, R. Han, Z. Hu, X. Chen, D. Sun, R. Zhang, D. Chen, D. Chen, X. Chen, J. Liang, F. Cao, and J. Tian, “In vivo quantitative bioluminescence tomography using heterogeneous and homogeneous mouse models,” Opt. Express 18(12), 13102–13113 (2010).
[Crossref] [PubMed]

Li, Y.

P. Wu, K. Liu, Q. Zhang, Z. Xue, Y. Li, N. Ning, X. Yang, X. Li, and J. Tian, “Detection of mouse liver cancer via a parallel iterative shrinkage method in hybrid optical/microcomputed tomography imaging,” J. Biomed. Opt. 17(12), 126012 (2012).
[Crossref] [PubMed]

G. Wang, Y. Li, and M. Jiang, “Uniqueness theorems in bioluminescence tomography,” Med. Phys. 31(8), 2289–2299 (2004).
[Crossref] [PubMed]

Liang, J.

Liang, J. M.

G. Wang, W. X. Cong, Q. S. Yang, Q. Pian, S. P. Zhu, J. M. Liang, M. Barroso, and X. Intes, “Innovation and fusion of X-ray and optical tomography for mouse studies of breast cancer,” Proc. SPIE 9967, 99671R (2016).
[Crossref]

Lieuwes, N. G.

S. Yahyanejad, P. V. Granton, N. G. Lieuwes, L. Gilmour, L. Dubois, J. Theys, A. J. Chalmers, F. Verhaegen, and M. Vooijs, “Complementary use of bioluminescence imaging and contrast-enhanced micro-computed tomography in an orthotopic brain tumor model,” Mol. Imaging 13(1), 1–8 (2014).
[PubMed]

Lin, Y.

H. Yan, Y. Lin, W. C. Barber, M. B. Unlu, and G. Gulsen, “A gantry-based tri-modality system for bioluminescence tomography,” Rev. Sci. Instrum. 83(4), 043708 (2012).
[Crossref] [PubMed]

Liu, F.

Liu, H.

S. Zhang, K. Wang, H. Liu, C. Leng, Y. Gao, and J. Tian, “Reconstruction method for in vivo bioluminescence tomography based on the split Bregman iterative and surrogate functions,” Mol. Imaging Biol. 19(2), 245–255 (2017).
[Crossref] [PubMed]

Liu, J.

Liu, K.

P. Wu, K. Liu, Q. Zhang, Z. Xue, Y. Li, N. Ning, X. Yang, X. Li, and J. Tian, “Detection of mouse liver cancer via a parallel iterative shrinkage method in hybrid optical/microcomputed tomography imaging,” J. Biomed. Opt. 17(12), 126012 (2012).
[Crossref] [PubMed]

K. Liu, Y. Lu, J. Tian, C. Qin, X. Yang, S. Zhu, X. Yang, Q. Gao, and D. Han, “Evaluation of the simplified spherical harmonics approximation in bioluminescence tomography through heterogeneous mouse models,” Opt. Express 18(20), 20988–21002 (2010).
[Crossref] [PubMed]

Liu, L.

Liu, Y.

Löwik, C. W.

M. Baiker, M. Staring, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Automated registration of whole-body follow-up MicroCT data of mice,” Med Image Comput Comput Assist Interv 14(Pt 2), 516–523 (2011).
[PubMed]

M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
[Crossref] [PubMed]

Lu, Y.

C. Darne, Y. Lu, and E. M. Sevick-Muraca, “Small animal fluorescence and bioluminescence tomography: a review of approaches, algorithms and technology update,” Phys. Med. Biol. 59(1), R1–R64 (2014).
[Crossref] [PubMed]

K. Liu, Y. Lu, J. Tian, C. Qin, X. Yang, S. Zhu, X. Yang, Q. Gao, and D. Han, “Evaluation of the simplified spherical harmonics approximation in bioluminescence tomography through heterogeneous mouse models,” Opt. Express 18(20), 20988–21002 (2010).
[Crossref] [PubMed]

Luo, J.

Ma, W.

Ma, X.

Ma, X. B.

C. H. Qin, J. C. Feng, S. P. Zhu, X. B. Ma, J. H. Zhong, P. Wu, Z. Y. Jin, and J. Tian, “Recent advances in bioluminescence tomography: methodology and system as well as application,” Laser Photonics Rev. 8(1), 94–114 (2014).
[Crossref]

Maafi, F.

Malek, R.

B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
[Crossref] [PubMed]

Mao, Y.

Mastanduno, M. A.

M. Jermyn, H. Ghadyani, M. A. Mastanduno, W. Turner, S. C. Davis, H. Dehghani, and B. W. Pogue, “Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography,” J. Biomed. Opt. 18(8), 086007 (2013).
[Crossref] [PubMed]

McCray, P.

McLennan, G.

Meng, M.

Meyer, C. R.

H. Park, P. H. Bland, and C. R. Meyer, “Construction of an abdominal probabilistic atlas and its application in segmentation,” IEEE Trans. Med. Imaging 22(4), 483–492 (2003).
[Crossref] [PubMed]

Milles, J.

M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
[Crossref] [PubMed]

Naser, M. A.

M. A. Naser, M. S. Patterson, and J. W. Wong, “Algorithm for localized adaptive diffuse optical tomography and its application in bioluminescence tomography,” Phys. Med. Biol. 59(8), 2089–2109 (2014).
[Crossref] [PubMed]

Ning, N.

P. Wu, K. Liu, Q. Zhang, Z. Xue, Y. Li, N. Ning, X. Yang, X. Li, and J. Tian, “Detection of mouse liver cancer via a parallel iterative shrinkage method in hybrid optical/microcomputed tomography imaging,” J. Biomed. Opt. 17(12), 126012 (2012).
[Crossref] [PubMed]

Ntziachristos, V.

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]

Park, H.

H. Park, P. H. Bland, and C. R. Meyer, “Construction of an abdominal probabilistic atlas and its application in segmentation,” IEEE Trans. Med. Imaging 22(4), 483–492 (2003).
[Crossref] [PubMed]

Patterson, M. S.

B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
[Crossref] [PubMed]

M. A. Naser, M. S. Patterson, and J. W. Wong, “Algorithm for localized adaptive diffuse optical tomography and its application in bioluminescence tomography,” Phys. Med. Biol. 59(8), 2089–2109 (2014).
[Crossref] [PubMed]

H. Dehghani, S. C. Davis, S. Jiang, B. W. Pogue, K. D. Paulsen, and M. S. Patterson, “Spectrally resolved bioluminescence optical tomography,” Opt. Lett. 31(3), 365–367 (2006).
[Crossref] [PubMed]

Paulsen, K. D.

H. Dehghani, M. E. Eames, P. K. Yalavarthy, S. C. Davis, S. Srinivasan, C. M. Carpenter, B. W. Pogue, and K. D. Paulsen, “Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction,” Commun. Numer. Methods Eng. 25(6), 711–732 (2008).
[Crossref] [PubMed]

H. Dehghani, S. C. Davis, S. Jiang, B. W. Pogue, K. D. Paulsen, and M. S. Patterson, “Spectrally resolved bioluminescence optical tomography,” Opt. Lett. 31(3), 365–367 (2006).
[Crossref] [PubMed]

Pian, Q.

G. Wang, W. X. Cong, Q. S. Yang, Q. Pian, S. P. Zhu, J. M. Liang, M. Barroso, and X. Intes, “Innovation and fusion of X-ray and optical tomography for mouse studies of breast cancer,” Proc. SPIE 9967, 99671R (2016).
[Crossref]

Platero, C.

C. Platero and M. C. Tobar, “A multi-atlas segmentation using graph cuts with applications to liver segmentation in CT scans,” Comput. Math. Methods Med. 2014, 182909 (2014).
[Crossref] [PubMed]

Pogue, B. W.

M. Jermyn, H. Ghadyani, M. A. Mastanduno, W. Turner, S. C. Davis, H. Dehghani, and B. W. Pogue, “Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography,” J. Biomed. Opt. 18(8), 086007 (2013).
[Crossref] [PubMed]

H. Dehghani, M. E. Eames, P. K. Yalavarthy, S. C. Davis, S. Srinivasan, C. M. Carpenter, B. W. Pogue, and K. D. Paulsen, “Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction,” Commun. Numer. Methods Eng. 25(6), 711–732 (2008).
[Crossref] [PubMed]

H. Dehghani, S. C. Davis, S. Jiang, B. W. Pogue, K. D. Paulsen, and M. S. Patterson, “Spectrally resolved bioluminescence optical tomography,” Opt. Lett. 31(3), 365–367 (2006).
[Crossref] [PubMed]

Pollack, A.

J. Shi, T. S. Udayakumar, K. Xu, N. Dogan, A. Pollack, and Y. Yang, “Bioluminescence tomography guided small-animal radiation therapy and tumor response assessment,” Int. J. Radiat. Oncol. Biol. Phys. S0360-3016(18)30182-2, epub ahead of print (2018).
[PubMed]

Ponomarev, V.

A. D. Klose, B. J. Beattie, H. Dehghani, L. Vider, C. Le, V. Ponomarev, and R. Blasberg, “In vivo bioluminescence tomography with a blocking-off finite-difference SP3 method and MRI/CT coregistration,” Med. Phys. 37(1), 329–338 (2010).
[Crossref] [PubMed]

Pouliot, P.

Qi, J.

Qian, X.

Qin, C.

Qin, C. H.

C. H. Qin, J. C. Feng, S. P. Zhu, X. B. Ma, J. H. Zhong, P. Wu, Z. Y. Jin, and J. Tian, “Recent advances in bioluminescence tomography: methodology and system as well as application,” Laser Photonics Rev. 8(1), 94–114 (2014).
[Crossref]

Qu, X.

Que, I.

M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
[Crossref] [PubMed]

Rannou, F. R.

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]

Reiber, J. H.

M. Baiker, M. Staring, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Automated registration of whole-body follow-up MicroCT data of mice,” Med Image Comput Comput Assist Interv 14(Pt 2), 516–523 (2011).
[PubMed]

M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
[Crossref] [PubMed]

Ren, S.

Reyes, J.

B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
[Crossref] [PubMed]

Rhéaume, E.

Rice, B. W.

C. Kuo, O. Coquoz, T. L. Troy, H. Xu, and B. W. Rice, “Three-dimensional reconstruction of in vivo bioluminescent sources based on multispectral imaging,” J. Biomed. Opt. 12(2), 024007 (2007).
[Crossref] [PubMed]

Salvado, O.

D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, H. Green, M. C. Gregoire, and O. Salvado, “Mouse whole-body organ mapping by non-rigid registration approach,” Proc. SPIE 7965, 79650E (2011).
[Crossref]

Sarkar, S.

S. M. Hejazi, S. Sarkar, and Z. Darezereshki, “Fast multislice fluorescence molecular tomography using sparsity-inducing regularization,” J. Biomed. Opt. 21(2), 026012 (2016).
[Crossref] [PubMed]

Segars, W. P.

W. P. Segars, B. M. 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]

Sevick-Muraca, E. M.

C. Darne, Y. Lu, and E. M. Sevick-Muraca, “Small animal fluorescence and bioluminescence tomography: a review of approaches, algorithms and technology update,” Phys. Med. Biol. 59(1), R1–R64 (2014).
[Crossref] [PubMed]

Shen, H.

Shi, J.

J. Shi, B. Zhang, F. Liu, J. Luo, and J. Bai, “Efficient L1 regularization-based reconstruction for fluorescent molecular tomography using restarted nonlinear conjugate gradient,” Opt. Lett. 38(18), 3696–3699 (2013).
[Crossref] [PubMed]

J. Shi, T. S. Udayakumar, K. Xu, N. Dogan, A. Pollack, and Y. Yang, “Bioluminescence tomography guided small-animal radiation therapy and tumor response assessment,” Int. J. Radiat. Oncol. Biol. Phys. S0360-3016(18)30182-2, epub ahead of print (2018).
[PubMed]

Sinn, P.

Srinivasan, S.

H. Dehghani, M. E. Eames, P. K. Yalavarthy, S. C. Davis, S. Srinivasan, C. M. Carpenter, B. W. Pogue, and K. D. Paulsen, “Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction,” Commun. Numer. Methods Eng. 25(6), 711–732 (2008).
[Crossref] [PubMed]

Staring, M.

M. Baiker, M. Staring, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Automated registration of whole-body follow-up MicroCT data of mice,” Med Image Comput Comput Assist Interv 14(Pt 2), 516–523 (2011).
[PubMed]

Stout, D.

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]

Stout, D. B.

H. Wang, D. B. Stout, and A. F. Chatziioannou, “A deformable atlas of the laboratory mouse,” Mol. Imaging Biol. 17(1), 18–28 (2015).
[Crossref] [PubMed]

H. Wang, D. B. Stout, and A. F. Chatziioannou, “Estimation of mouse organ locations through registration of a statistical mouse atlas with micro-CT images,” IEEE Trans. Med. Imaging 31(1), 88–102 (2012).
[Crossref] [PubMed]

Sun, D.

Tamayo, O. A.

D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, H. Green, M. C. Gregoire, and O. Salvado, “Mouse whole-body organ mapping by non-rigid registration approach,” Proc. SPIE 7965, 79650E (2011).
[Crossref]

Tardif, J. C.

Theys, J.

S. Yahyanejad, P. V. Granton, N. G. Lieuwes, L. Gilmour, L. Dubois, J. Theys, A. J. Chalmers, F. Verhaegen, and M. Vooijs, “Complementary use of bioluminescence imaging and contrast-enhanced micro-computed tomography in an orthotopic brain tumor model,” Mol. Imaging 13(1), 1–8 (2014).
[PubMed]

Tian, J.

S. Zhang, K. Wang, H. Liu, C. Leng, Y. Gao, and J. Tian, “Reconstruction method for in vivo bioluminescence tomography based on the split Bregman iterative and surrogate functions,” Mol. Imaging Biol. 19(2), 245–255 (2017).
[Crossref] [PubMed]

S. Jiang, J. Liu, Y. An, G. Zhang, J. Ye, Y. Mao, K. He, C. Chi, and J. Tian, “Novel l 2,1-norm optimization method for fluorescence molecular tomography reconstruction,” Biomed. Opt. Express 7(6), 2342–2359 (2016).
[Crossref] [PubMed]

J. Zhang, D. Chen, J. Liang, H. Xue, J. Lei, Q. Wang, D. Chen, M. Meng, Z. Jin, and J. Tian, “Incorporating MRI structural information into bioluminescence tomography: system, heterogeneous reconstruction and in vivo quantification,” Biomed. Opt. Express 5(6), 1861–1876 (2014).
[Crossref] [PubMed]

C. H. Qin, J. C. Feng, S. P. Zhu, X. B. Ma, J. H. Zhong, P. Wu, Z. Y. Jin, and J. Tian, “Recent advances in bioluminescence tomography: methodology and system as well as application,” Laser Photonics Rev. 8(1), 94–114 (2014).
[Crossref]

P. Wu, K. Liu, Q. Zhang, Z. Xue, Y. Li, N. Ning, X. Yang, X. Li, and J. Tian, “Detection of mouse liver cancer via a parallel iterative shrinkage method in hybrid optical/microcomputed tomography imaging,” J. Biomed. Opt. 17(12), 126012 (2012).
[Crossref] [PubMed]

Q. Zhang, X. Chen, X. Qu, J. Liang, and J. Tian, “Comparative studies of l(p)-regularization-based reconstruction algorithms for bioluminescence tomography,” Biomed. Opt. Express 3(11), 2916–2936 (2012).
[Crossref] [PubMed]

X. He, J. Liang, X. Wang, J. Yu, X. Qu, X. Wang, Y. Hou, D. Chen, F. Liu, and J. Tian, “Sparse reconstruction for quantitative bioluminescence tomography based on the incomplete variables truncated conjugate gradient method,” Opt. Express 18(24), 24825–24841 (2010).
[Crossref] [PubMed]

K. Liu, Y. Lu, J. Tian, C. Qin, X. Yang, S. Zhu, X. Yang, Q. Gao, and D. Han, “Evaluation of the simplified spherical harmonics approximation in bioluminescence tomography through heterogeneous mouse models,” Opt. Express 18(20), 20988–21002 (2010).
[Crossref] [PubMed]

J. Liu, Y. Wang, X. Qu, X. Li, X. Ma, R. Han, Z. Hu, X. Chen, D. Sun, R. Zhang, D. Chen, D. Chen, X. Chen, J. Liang, F. Cao, and J. Tian, “In vivo quantitative bioluminescence tomography using heterogeneous and homogeneous mouse models,” Opt. Express 18(12), 13102–13113 (2010).
[Crossref] [PubMed]

Tobar, M. C.

C. Platero and M. C. Tobar, “A multi-atlas segmentation using graph cuts with applications to liver segmentation in CT scans,” Comput. Math. Methods Med. 2014, 182909 (2014).
[Crossref] [PubMed]

Tran, P. T.

B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
[Crossref] [PubMed]

Troy, T. L.

C. Kuo, O. Coquoz, T. L. Troy, H. Xu, and B. W. Rice, “Three-dimensional reconstruction of in vivo bioluminescent sources based on multispectral imaging,” J. Biomed. Opt. 12(2), 024007 (2007).
[Crossref] [PubMed]

Tsui, B. M.

W. P. Segars, B. M. 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]

Turner, W.

M. Jermyn, H. Ghadyani, M. A. Mastanduno, W. Turner, S. C. Davis, H. Dehghani, and B. W. Pogue, “Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography,” J. Biomed. Opt. 18(8), 086007 (2013).
[Crossref] [PubMed]

Udayakumar, T. S.

J. Shi, T. S. Udayakumar, K. Xu, N. Dogan, A. Pollack, and Y. Yang, “Bioluminescence tomography guided small-animal radiation therapy and tumor response assessment,” Int. J. Radiat. Oncol. Biol. Phys. S0360-3016(18)30182-2, epub ahead of print (2018).
[PubMed]

Unlu, M. B.

H. Yan, Y. Lin, W. C. Barber, M. B. Unlu, and G. Gulsen, “A gantry-based tri-modality system for bioluminescence tomography,” Rev. Sci. Instrum. 83(4), 043708 (2012).
[Crossref] [PubMed]

Verhaegen, F.

S. Yahyanejad, P. V. Granton, N. G. Lieuwes, L. Gilmour, L. Dubois, J. Theys, A. J. Chalmers, F. Verhaegen, and M. Vooijs, “Complementary use of bioluminescence imaging and contrast-enhanced micro-computed tomography in an orthotopic brain tumor model,” Mol. Imaging 13(1), 1–8 (2014).
[PubMed]

Vider, L.

A. D. Klose, B. J. Beattie, H. Dehghani, L. Vider, C. Le, V. Ponomarev, and R. Blasberg, “In vivo bioluminescence tomography with a blocking-off finite-difference SP3 method and MRI/CT coregistration,” Med. Phys. 37(1), 329–338 (2010).
[Crossref] [PubMed]

Vooijs, M.

S. Yahyanejad, P. V. Granton, N. G. Lieuwes, L. Gilmour, L. Dubois, J. Theys, A. J. Chalmers, F. Verhaegen, and M. Vooijs, “Complementary use of bioluminescence imaging and contrast-enhanced micro-computed tomography in an orthotopic brain tumor model,” Mol. Imaging 13(1), 1–8 (2014).
[PubMed]

Wan, W.

Wang, G.

G. Wang, W. X. Cong, Q. S. Yang, Q. Pian, S. P. Zhu, J. M. Liang, M. Barroso, and X. Intes, “Innovation and fusion of X-ray and optical tomography for mouse studies of breast cancer,” Proc. SPIE 9967, 99671R (2016).
[Crossref]

G. Wang, W. Cong, K. Durairaj, X. Qian, H. Shen, P. Sinn, E. Hoffman, G. McLennan, and M. Henry, “In vivo mouse studies with bioluminescence tomography,” Opt. Express 14(17), 7801–7809 (2006).
[Crossref] [PubMed]

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. Wang, Y. Li, and M. Jiang, “Uniqueness theorems in bioluminescence tomography,” Med. Phys. 31(8), 2289–2299 (2004).
[Crossref] [PubMed]

Wang, H.

H. Wang, D. B. Stout, and A. F. Chatziioannou, “A deformable atlas of the laboratory mouse,” Mol. Imaging Biol. 17(1), 18–28 (2015).
[Crossref] [PubMed]

H. Wang, D. B. Stout, and A. F. Chatziioannou, “Estimation of mouse organ locations through registration of a statistical mouse atlas with micro-CT images,” IEEE Trans. Med. Imaging 31(1), 88–102 (2012).
[Crossref] [PubMed]

Wang, K.

S. Zhang, K. Wang, H. Liu, C. Leng, Y. Gao, and J. Tian, “Reconstruction method for in vivo bioluminescence tomography based on the split Bregman iterative and surrogate functions,” Mol. Imaging Biol. 19(2), 245–255 (2017).
[Crossref] [PubMed]

Wang, K. K.

B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
[Crossref] [PubMed]

Wang, L.

Wang, Q.

Wang, X.

Wang, Y.

Weber, A. W.

M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
[Crossref] [PubMed]

Wong, J. W.

B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
[Crossref] [PubMed]

M. A. Naser, M. S. Patterson, and J. W. Wong, “Algorithm for localized adaptive diffuse optical tomography and its application in bioluminescence tomography,” Phys. Med. Biol. 59(8), 2089–2109 (2014).
[Crossref] [PubMed]

Wu, P.

C. H. Qin, J. C. Feng, S. P. Zhu, X. B. Ma, J. H. Zhong, P. Wu, Z. Y. Jin, and J. Tian, “Recent advances in bioluminescence tomography: methodology and system as well as application,” Laser Photonics Rev. 8(1), 94–114 (2014).
[Crossref]

P. Wu, K. Liu, Q. Zhang, Z. Xue, Y. Li, N. Ning, X. Yang, X. Li, and J. Tian, “Detection of mouse liver cancer via a parallel iterative shrinkage method in hybrid optical/microcomputed tomography imaging,” J. Biomed. Opt. 17(12), 126012 (2012).
[Crossref] [PubMed]

Xiao, D.

D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, H. Green, M. C. Gregoire, and O. Salvado, “Mouse whole-body organ mapping by non-rigid registration approach,” Proc. SPIE 7965, 79650E (2011).
[Crossref]

Xu, H.

C. Kuo, O. Coquoz, T. L. Troy, H. Xu, and B. W. Rice, “Three-dimensional reconstruction of in vivo bioluminescent sources based on multispectral imaging,” J. Biomed. Opt. 12(2), 024007 (2007).
[Crossref] [PubMed]

Xu, K.

J. Shi, T. S. Udayakumar, K. Xu, N. Dogan, A. Pollack, and Y. Yang, “Bioluminescence tomography guided small-animal radiation therapy and tumor response assessment,” Int. J. Radiat. Oncol. Biol. Phys. S0360-3016(18)30182-2, epub ahead of print (2018).
[PubMed]

Xue, H.

Xue, Z.

P. Wu, K. Liu, Q. Zhang, Z. Xue, Y. Li, N. Ning, X. Yang, X. Li, and J. Tian, “Detection of mouse liver cancer via a parallel iterative shrinkage method in hybrid optical/microcomputed tomography imaging,” J. Biomed. Opt. 17(12), 126012 (2012).
[Crossref] [PubMed]

Yahyanejad, S.

S. Yahyanejad, P. V. Granton, N. G. Lieuwes, L. Gilmour, L. Dubois, J. Theys, A. J. Chalmers, F. Verhaegen, and M. Vooijs, “Complementary use of bioluminescence imaging and contrast-enhanced micro-computed tomography in an orthotopic brain tumor model,” Mol. Imaging 13(1), 1–8 (2014).
[PubMed]

Yalavarthy, P. K.

H. Dehghani, M. E. Eames, P. K. Yalavarthy, S. C. Davis, S. Srinivasan, C. M. Carpenter, B. W. Pogue, and K. D. Paulsen, “Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction,” Commun. Numer. Methods Eng. 25(6), 711–732 (2008).
[Crossref] [PubMed]

Yan, H.

H. Yan, Y. Lin, W. C. Barber, M. B. Unlu, and G. Gulsen, “A gantry-based tri-modality system for bioluminescence tomography,” Rev. Sci. Instrum. 83(4), 043708 (2012).
[Crossref] [PubMed]

Yang, Q. S.

G. Wang, W. X. Cong, Q. S. Yang, Q. Pian, S. P. Zhu, J. M. Liang, M. Barroso, and X. Intes, “Innovation and fusion of X-ray and optical tomography for mouse studies of breast cancer,” Proc. SPIE 9967, 99671R (2016).
[Crossref]

Yang, X.

Yang, Y.

J. Shi, T. S. Udayakumar, K. Xu, N. Dogan, A. Pollack, and Y. Yang, “Bioluminescence tomography guided small-animal radiation therapy and tumor response assessment,” Int. J. Radiat. Oncol. Biol. Phys. S0360-3016(18)30182-2, epub ahead of print (2018).
[PubMed]

Ye, J.

Yin, W. T.

W. T. Yin, “Analysis and generalizations of the linearized Bregman method,” SIAM J. Imaging Sci. 3(4), 856–877 (2010).
[Crossref]

Yu, D.

C. Leng, D. Yu, S. Zhang, Y. An, and Y. Hu, “Reconstruction method for optical tomography based on the linearized Bregman iteration with sparse regularization,” Comput. Math. Methods Med. 2015, 304191 (2015).
[Crossref] [PubMed]

Yu, J.

B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
[Crossref] [PubMed]

X. He, J. Liang, X. Wang, J. Yu, X. Qu, X. Wang, Y. Hou, D. Chen, F. Liu, and J. Tian, “Sparse reconstruction for quantitative bioluminescence tomography based on the incomplete variables truncated conjugate gradient method,” Opt. Express 18(24), 24825–24841 (2010).
[Crossref] [PubMed]

Zabner, J.

Zahra, D.

D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, H. Green, M. C. Gregoire, and O. Salvado, “Mouse whole-body organ mapping by non-rigid registration approach,” Proc. SPIE 7965, 79650E (2011).
[Crossref]

Zhang, B.

B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
[Crossref] [PubMed]

J. Shi, B. Zhang, F. Liu, J. Luo, and J. Bai, “Efficient L1 regularization-based reconstruction for fluorescent molecular tomography using restarted nonlinear conjugate gradient,” Opt. Lett. 38(18), 3696–3699 (2013).
[Crossref] [PubMed]

Zhang, G.

Zhang, J.

Zhang, L.

Zhang, Q.

Q. Zhang, X. Chen, X. Qu, J. Liang, and J. Tian, “Comparative studies of l(p)-regularization-based reconstruction algorithms for bioluminescence tomography,” Biomed. Opt. Express 3(11), 2916–2936 (2012).
[Crossref] [PubMed]

P. Wu, K. Liu, Q. Zhang, Z. Xue, Y. Li, N. Ning, X. Yang, X. Li, and J. Tian, “Detection of mouse liver cancer via a parallel iterative shrinkage method in hybrid optical/microcomputed tomography imaging,” J. Biomed. Opt. 17(12), 126012 (2012).
[Crossref] [PubMed]

Zhang, R.

Zhang, S.

S. Zhang, K. Wang, H. Liu, C. Leng, Y. Gao, and J. Tian, “Reconstruction method for in vivo bioluminescence tomography based on the split Bregman iterative and surrogate functions,” Mol. Imaging Biol. 19(2), 245–255 (2017).
[Crossref] [PubMed]

C. Leng, D. Yu, S. Zhang, Y. An, and Y. Hu, “Reconstruction method for optical tomography based on the linearized Bregman iteration with sparse regularization,” Comput. Math. Methods Med. 2015, 304191 (2015).
[Crossref] [PubMed]

Zhao, H.

Zhong, J. H.

C. H. Qin, J. C. Feng, S. P. Zhu, X. B. Ma, J. H. Zhong, P. Wu, Z. Y. Jin, and J. Tian, “Recent advances in bioluminescence tomography: methodology and system as well as application,” Laser Photonics Rev. 8(1), 94–114 (2014).
[Crossref]

Zhou, Z.

Zhu, S.

Zhu, S. P.

G. Wang, W. X. Cong, Q. S. Yang, Q. Pian, S. P. Zhu, J. M. Liang, M. Barroso, and X. Intes, “Innovation and fusion of X-ray and optical tomography for mouse studies of breast cancer,” Proc. SPIE 9967, 99671R (2016).
[Crossref]

C. H. Qin, J. C. Feng, S. P. Zhu, X. B. Ma, J. H. Zhong, P. Wu, Z. Y. Jin, and J. Tian, “Recent advances in bioluminescence tomography: methodology and system as well as application,” Laser Photonics Rev. 8(1), 94–114 (2014).
[Crossref]

Biomed. Opt. Express (6)

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]

J. Zhang, D. Chen, J. Liang, H. Xue, J. Lei, Q. Wang, D. Chen, M. Meng, Z. Jin, and J. Tian, “Incorporating MRI structural information into bioluminescence tomography: system, heterogeneous reconstruction and in vivo quantification,” Biomed. Opt. Express 5(6), 1861–1876 (2014).
[Crossref] [PubMed]

W. Wan, Y. Wang, J. Qi, L. Liu, W. Ma, J. Li, L. Zhang, Z. Zhou, H. Zhao, and F. Gao, “Region-based diffuse optical tomography with registered atlas: in vivo acquisition of mouse optical properties,” Biomed. Opt. Express 7(12), 5066–5080 (2016).
[Crossref] [PubMed]

S. Ren, H. Hu, G. Li, X. Cao, S. Zhu, X. Chen, and J. Liang, “Multi-atlas registration and adaptive hexahedral voxel discretization for fast bioluminescence tomography,” Biomed. Opt. Express 7(4), 1549–1560 (2016).
[Crossref] [PubMed]

Q. Zhang, X. Chen, X. Qu, J. Liang, and J. Tian, “Comparative studies of l(p)-regularization-based reconstruction algorithms for bioluminescence tomography,” Biomed. Opt. Express 3(11), 2916–2936 (2012).
[Crossref] [PubMed]

S. Jiang, J. Liu, Y. An, G. Zhang, J. Ye, Y. Mao, K. He, C. Chi, and J. Tian, “Novel l 2,1-norm optimization method for fluorescence molecular tomography reconstruction,” Biomed. Opt. Express 7(6), 2342–2359 (2016).
[Crossref] [PubMed]

Commun. Numer. Methods Eng. (1)

H. Dehghani, M. E. Eames, P. K. Yalavarthy, S. C. Davis, S. Srinivasan, C. M. Carpenter, B. W. Pogue, and K. D. Paulsen, “Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction,” Commun. Numer. Methods Eng. 25(6), 711–732 (2008).
[Crossref] [PubMed]

Comput. Math. Methods Med. (2)

C. Leng, D. Yu, S. Zhang, Y. An, and Y. Hu, “Reconstruction method for optical tomography based on the linearized Bregman iteration with sparse regularization,” Comput. Math. Methods Med. 2015, 304191 (2015).
[Crossref] [PubMed]

C. Platero and M. C. Tobar, “A multi-atlas segmentation using graph cuts with applications to liver segmentation in CT scans,” Comput. Math. Methods Med. 2014, 182909 (2014).
[Crossref] [PubMed]

IEEE Trans. Med. Imaging (2)

H. Wang, D. B. Stout, and A. F. Chatziioannou, “Estimation of mouse organ locations through registration of a statistical mouse atlas with micro-CT images,” IEEE Trans. Med. Imaging 31(1), 88–102 (2012).
[Crossref] [PubMed]

H. Park, P. H. Bland, and C. R. Meyer, “Construction of an abdominal probabilistic atlas and its application in segmentation,” IEEE Trans. Med. Imaging 22(4), 483–492 (2003).
[Crossref] [PubMed]

Int. J. Radiat. Oncol. Biol. Phys. (1)

B. Zhang, K. K. Wang, J. Yu, S. Eslami, I. Iordachita, J. Reyes, R. Malek, P. T. Tran, M. S. Patterson, and J. W. Wong, “Bioluminescence tomography-guided radiation therapy for preclinical research,” Int. J. Radiat. Oncol. Biol. Phys. 94(5), 1144–1153 (2016).
[Crossref] [PubMed]

J. Biomed. Opt. (4)

P. Wu, K. Liu, Q. Zhang, Z. Xue, Y. Li, N. Ning, X. Yang, X. Li, and J. Tian, “Detection of mouse liver cancer via a parallel iterative shrinkage method in hybrid optical/microcomputed tomography imaging,” J. Biomed. Opt. 17(12), 126012 (2012).
[Crossref] [PubMed]

C. Kuo, O. Coquoz, T. L. Troy, H. Xu, and B. W. Rice, “Three-dimensional reconstruction of in vivo bioluminescent sources based on multispectral imaging,” J. Biomed. Opt. 12(2), 024007 (2007).
[Crossref] [PubMed]

M. Jermyn, H. Ghadyani, M. A. Mastanduno, W. Turner, S. C. Davis, H. Dehghani, and B. W. Pogue, “Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography,” J. Biomed. Opt. 18(8), 086007 (2013).
[Crossref] [PubMed]

S. M. Hejazi, S. Sarkar, and Z. Darezereshki, “Fast multislice fluorescence molecular tomography using sparsity-inducing regularization,” J. Biomed. Opt. 21(2), 026012 (2016).
[Crossref] [PubMed]

J. Comput. Phys. (1)

A. D. Klose and E. W. Larsen, “Light transport in biological tissue based on the simplified spherical harmonics equations,” J. Comput. Phys. 220(1), 441–470 (2006).
[Crossref]

Laser Photonics Rev. (1)

C. H. Qin, J. C. Feng, S. P. Zhu, X. B. Ma, J. H. Zhong, P. Wu, Z. Y. Jin, and J. Tian, “Recent advances in bioluminescence tomography: methodology and system as well as application,” Laser Photonics Rev. 8(1), 94–114 (2014).
[Crossref]

Med Image Comput Comput Assist Interv (1)

M. Baiker, M. Staring, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Automated registration of whole-body follow-up MicroCT data of mice,” Med Image Comput Comput Assist Interv 14(Pt 2), 516–523 (2011).
[PubMed]

Med. Image Anal. (1)

M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Löwik, J. H. Reiber, and B. P. Lelieveldt, “Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data,” Med. Image Anal. 14(6), 723–737 (2010).
[Crossref] [PubMed]

Med. Phys. (2)

G. Wang, Y. Li, and M. Jiang, “Uniqueness theorems in bioluminescence tomography,” Med. Phys. 31(8), 2289–2299 (2004).
[Crossref] [PubMed]

A. D. Klose, B. J. Beattie, H. Dehghani, L. Vider, C. Le, V. Ponomarev, and R. Blasberg, “In vivo bioluminescence tomography with a blocking-off finite-difference SP3 method and MRI/CT coregistration,” Med. Phys. 37(1), 329–338 (2010).
[Crossref] [PubMed]

Mol. Imaging (1)

S. Yahyanejad, P. V. Granton, N. G. Lieuwes, L. Gilmour, L. Dubois, J. Theys, A. J. Chalmers, F. Verhaegen, and M. Vooijs, “Complementary use of bioluminescence imaging and contrast-enhanced micro-computed tomography in an orthotopic brain tumor model,” Mol. Imaging 13(1), 1–8 (2014).
[PubMed]

Mol. Imaging Biol. (3)

H. Wang, D. B. Stout, and A. F. Chatziioannou, “A deformable atlas of the laboratory mouse,” Mol. Imaging Biol. 17(1), 18–28 (2015).
[Crossref] [PubMed]

W. P. Segars, B. M. 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]

S. Zhang, K. Wang, H. Liu, C. Leng, Y. Gao, and J. Tian, “Reconstruction method for in vivo bioluminescence tomography based on the split Bregman iterative and surrogate functions,” Mol. Imaging Biol. 19(2), 245–255 (2017).
[Crossref] [PubMed]

Nat. Methods (1)

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]

Opt. Express (6)

J. Liu, Y. Wang, X. Qu, X. Li, X. Ma, R. Han, Z. Hu, X. Chen, D. Sun, R. Zhang, D. Chen, D. Chen, X. Chen, J. Liang, F. Cao, and J. Tian, “In vivo quantitative bioluminescence tomography using heterogeneous and homogeneous mouse models,” Opt. Express 18(12), 13102–13113 (2010).
[Crossref] [PubMed]

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. Wang, W. Cong, K. Durairaj, X. Qian, H. Shen, P. Sinn, E. Hoffman, G. McLennan, and M. Henry, “In vivo mouse studies with bioluminescence tomography,” Opt. Express 14(17), 7801–7809 (2006).
[Crossref] [PubMed]

K. Liu, Y. Lu, J. Tian, C. Qin, X. Yang, S. Zhu, X. Yang, Q. Gao, and D. Han, “Evaluation of the simplified spherical harmonics approximation in bioluminescence tomography through heterogeneous mouse models,” Opt. Express 18(20), 20988–21002 (2010).
[Crossref] [PubMed]

H. Gao and H. Zhao, “Multilevel bioluminescence tomography based on radiative transfer equation Part 1: l1 regularization,” Opt. Express 18(3), 1854–1871 (2010).
[Crossref] [PubMed]

X. He, J. Liang, X. Wang, J. Yu, X. Qu, X. Wang, Y. Hou, D. Chen, F. Liu, and J. Tian, “Sparse reconstruction for quantitative bioluminescence tomography based on the incomplete variables truncated conjugate gradient method,” Opt. Express 18(24), 24825–24841 (2010).
[Crossref] [PubMed]

Opt. Lett. (2)

Phys. Med. Biol. (5)

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]

C. Darne, Y. Lu, and E. M. Sevick-Muraca, “Small animal fluorescence and bioluminescence tomography: a review of approaches, algorithms and technology update,” Phys. Med. Biol. 59(1), R1–R64 (2014).
[Crossref] [PubMed]

M. A. Naser, M. S. Patterson, and J. W. Wong, “Algorithm for localized adaptive diffuse optical tomography and its application in bioluminescence tomography,” Phys. Med. Biol. 59(8), 2089–2109 (2014).
[Crossref] [PubMed]

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

Proc. SPIE (3)

G. Wang, W. X. Cong, Q. S. Yang, Q. Pian, S. P. Zhu, J. M. Liang, M. Barroso, and X. Intes, “Innovation and fusion of X-ray and optical tomography for mouse studies of breast cancer,” Proc. SPIE 9967, 99671R (2016).
[Crossref]

A. J. Chaudhari, A. A. Joshi, F. Darvas, and R. M. Leahy, “A method for atlas-based volumetric registration with surface constraints for optical bioluminescence tomography in small animal imaging,” Proc. SPIE 6510, 651024 (2007).
[Crossref]

D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, H. Green, M. C. Gregoire, and O. Salvado, “Mouse whole-body organ mapping by non-rigid registration approach,” Proc. SPIE 7965, 79650E (2011).
[Crossref]

Rev. Sci. Instrum. (1)

H. Yan, Y. Lin, W. C. Barber, M. B. Unlu, and G. Gulsen, “A gantry-based tri-modality system for bioluminescence tomography,” Rev. Sci. Instrum. 83(4), 043708 (2012).
[Crossref] [PubMed]

SIAM J. Imaging Sci. (1)

W. T. Yin, “Analysis and generalizations of the linearized Bregman method,” SIAM J. Imaging Sci. 3(4), 856–877 (2010).
[Crossref]

Trends Mol. Med. (1)

M. Keyaerts, V. Caveliers, and T. Lahoutte, “Bioluminescence imaging: looking beyond the light,” Trends Mol. Med. 18(3), 164–172 (2012).
[Crossref] [PubMed]

Other (1)

J. Shi, T. S. Udayakumar, K. Xu, N. Dogan, A. Pollack, and Y. Yang, “Bioluminescence tomography guided small-animal radiation therapy and tumor response assessment,” Int. J. Radiat. Oncol. Biol. Phys. S0360-3016(18)30182-2, epub ahead of print (2018).
[PubMed]

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Figures (8)

Fig. 1
Fig. 1 Flow chart of BLT reconstruction based on statistical mouse atlas. (a) Construction of the statistical mouse atlas. (b) Organ registration by fitting the statistical mouse atlas. (c) Multispectral BLIs and the discretized mesh. (d) Mapping the BLIs to the mesh surface. (e) Reconstruction of the bioluminescent light source.
Fig. 2
Fig. 2 Organ localization through registration of a statistical mouse atlas. (a) Manually segmented 3D Digimouse (ground truth). (b) The estimated organs from the registered statistical mouse atlas, which is overlapped with the manually segmented organs. Only the torso region between the dish lines is analyzed. (c)-(e) The coronal, sagittal and transverse sections, respectively. (f) The discretized mesh of the manually segmented organs.
Fig. 3
Fig. 3 Scenario 1: Light source in the lung. (a1-a3) The transverse, coronal and sagittal sections of the sphere source. The estimated organs are fused with the ground truth. (b) The BLI is mapped on the mesh surface (only 610nm is shown). (c) BLT reconstruction with statistical mouse atlas. (d) BLT reconstruction with accurate organ segmentation. (e1-e2) The transverse and sagittal sections of the BLT (reconstructed with statistical mouse atlas) overlapped with CT images. (f1-f2) The transverse and sagittal sections of the BLT (reconstructed with accurate organ segmentation) overlapped with CT images.
Fig. 4
Fig. 4 Scenario 2: Light source in the liver, and the estimated organ is well registered. (a1-a3) The transverse, coronal and sagittal sections of the sphere source. The estimated organs are fused with the ground truth. (b) The BLI is mapped on the mesh surface (only 610nm is shown). BLT reconstruction with statistical mouse atlas (c) and accurate organ segmentation (d). (e1-e2) The transverse and sagittal sections of the BLT reconstructed with statistical mouse atlas overlapped with the CT images. (f1-f2) The BLT reconstructed with accurate organ segmentation overlapped with the CT images.
Fig. 5
Fig. 5 Scenario 3: Light source in the liver, and the estimated organ is not accurately registered. (a1-a3) The transverse, coronal and sagittal sections of the sphere source. The estimated organs are fused with the ground truth. (b) The BLI is mapped on the mesh surface (only 610nm is shown). BLT reconstruction with statistical mouse atlas (c) and accurate organ segmentation (d). (e1-e2) Fusion of BLT reconstructed with statistical mouse atlas with CT images. (f1-f2) Fusion of BLT reconstructed with accurate organ segmentation with the CT images.
Fig. 6
Fig. 6 Scenario 4: Light source in the kidney, and the estimated organ is not accurately registered. (a1-a3) The coronal, sagittal and transverse sections of the sphere source. The estimated organs are fused with the ground truth. (b) The BLI is mapped on the mesh surface (only 610nm is shown). BLT reconstruction with statistical mouse atlas (c) and accurate organ segmentation (d). (e1-e2) Fusion of BLT reconstructed with statistical mouse atlas with CT images. (f1-f2) Fusion of BLT reconstructed with accurate organ segmentation with the CT images.
Fig. 7
Fig. 7 Scenario 5: Two light sources in the lung. (a1-a2) The transverse and coronal sections of source 1 (s1). (b1-b2) The transverse and coronal sections of source 2 (s2). The estimated organs are fused with the ground truth. (c) The BLI is mapped on the mesh surface (only 610nm is shown). BLT reconstruction with statistical mouse atlas (d) and accurate organ segmentation (e). (f1-f4) Fusion of BLT reconstructed with statistical mouse atlas with CT images corresponding to s1 and s2. (g1-g4) Fusion of BLT reconstructed with accurate organ segmentation with the CT images.
Fig. 8
Fig. 8 Reconstruction results of the in vivo experiments. (a) Photo of the experimental mouse. (b1-b3) The coronal, transverse and sagittal sections of the imbedded source. (c1-c3) The coronal, transverse and sagittal sections of the mouse with estimated organs. (d) 3D rendering of the estimated organs. (e) The BLI (610nm) mapped on the mesh surface. (f) 3D rendering of the reconstructed source distribution. (g1-g3) Fusion of the BLT reconstructed bioluminescent source with the CBCT image.

Tables (3)

Tables Icon

Table 1 Optical properties of different organs at different wavelengths [39]

Tables Icon

Table 2 The reconstructed center of mass (CoM) and the 3D offset between the true source center and the BLT-reconstructed CoM for different scenarios

Tables Icon

Table 3 Quantitative comparison of the reconstructed sources for different scenarios

Equations (8)

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

{   1 3 μ a1   φ 1 (r)+ μ a φ 1 (r) 2 3 μ a φ 2 (r)=δ(r r S )   1 7 μ a3 φ 2 (r)+( 4 9 μ a + 5 9 μ a2 ) φ 2 (r) 2 3 μ a φ 1 (r)= 2 3 δ(r r S ) ,
ϕ 0 (r)=G( r S ,r)= φ 1 (r) 2 3 φ 2 (r).
J( r d )=Θ G(r, r d ) x(r)dr=Θ G( r d ,r) x(r)dr,
[ J 1 J M ]=[ G 1,1 G 1,N G M,1 G M,N ][ x 1 x N ],
[ J( λ 1 ) J( λ k ) ]=[ η( λ 1 )G( λ 1 ) η( λ k )G( λ k ) ][ x 1 x N ],
min x { x 1 :Gx=J },
min x { x 1 + 1 2α x 2 2 :Gx=J },
Dice=2 V rec V true V rec + V true