Joint L 1 and total variation regularization for fluorescence molecular tomography

Physics in Medicine and Biology

Volumn 57, Issue 6, 2012, Pages 1459-1476

  Dutta, Joyita ^a,b   Ahn, Sangtae ^a   Li, Changqing ^c   Cherry, Simon R ^c   Leahy, Richard M ^a  

^a University of Southern California   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c University of California Davis   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

3D VISUALIZATION; BACKGROUND SIGNALS; CONICAL MIRROR; COREGISTRATION; CT IMAGE; DEGREE OF ABSORPTION; EXPERIMENTAL DATA; FLUORESCENCE MOLECULAR TOMOGRAPHY; FLUORESCENT PROBES; ILL-CONDITIONED; IMAGING MODALITY; IN-VIVO; MINIMUM ENERGY; MOLECULAR TARGETS; NUMERICAL ERRORS; PERFORMANCE METRICS; PIECE-WISE; RECONSTRUCTED IMAGE; SEARCH SPACES; SIMILARITY COEFFICIENTS; SMALL ANIMAL; SOLUTION SET; SPECIFIC AREAS; SUPPRESS SPURIOUS; SURROGATE-BASED OPTIMIZATION; TISSUE OPTICAL PROPERTIES; TOTAL VARIATION NORM; TOTAL VARIATION REGULARIZATION;

ANIMALS; COMPUTERIZED TOMOGRAPHY; FLUORESCENCE; IMAGE DENOISING; IMAGE RECONSTRUCTION; INVERSE PROBLEMS; OPTICAL PROPERTIES; THREE DIMENSIONAL COMPUTER GRAPHICS; TISSUE; TOMOGRAPHY; VISUALIZATION;

THREE DIMENSIONAL;

ALGORITHM; ANIMAL; ARTICLE; COMPUTER ASSISTED TOMOGRAPHY; COMPUTER SIMULATION; FLUORESCENCE; IMAGE QUALITY; LIGHT RELATED PHENOMENA; METHODOLOGY; MOUSE; OPTICAL TOMOGRAPHY; STATISTICS; THREE DIMENSIONAL IMAGING; VALIDATION STUDY;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; FLUORESCENCE; IMAGING, THREE-DIMENSIONAL; MICE; OPTICAL PHENOMENA; PHANTOMS, IMAGING; TOMOGRAPHY, OPTICAL; TOMOGRAPHY, X-RAY COMPUTED;

EID: 84863238046     PISSN: 00319155     EISSN: 13616560     Source Type: Journal    
DOI: 10.1088/0031-9155/57/6/1459     Document Type: Article

References (62)

1. Ahn S and Fessler J 2003 Globally convergent image reconstruction for emission tomography using relaxed ordered subsets algorithms IEEE Trans. Med. Imaging 22 61326
2. Axelsson J, Svensson J and Andersson-Engels S 2007 Spatially varying regularization based on spectrally resolved fluorescence emission in fluorescence molecular tomography Opt. Express 15 1357484 (Pubitemid 47608567)
3. Beck A and Teboulle M 2009 A fast iterative shrinkage-thresholding algorithm for linear inverse problems SIAM J. Imaging Sci. 2 183202
4. B́langer S, Abran M, Intes X, Casanova C and Lesage F 2010 Real-time diffuse optical tomography based on structured illumination J. Biomed. Opt. 15 016006
5. Bertsekas D P 1999 Nonlinear Programming (Belmont, MA: Athena Scientific)
6. Bloch S, Lesage F, McIntosh L, Gandjbakhche A, Liang K and Achilefu S 2005 Whole-body fluorescence lifetime imaging of a tumor-targeted near-infrared molecular probe in mice J. Biomed. Opt. 10 054003
7. Candes E J and Wakin M B 2008 An introduction to compressive sampling IEEE Signal Process. Mag. 25 2130
8. Cao N, Nehorai A and Jacobs M 2007 Image reconstruction for diffuse optical tomography using sparsity regularization and expectation-maximization algorithm Opt. Express 15 13695708 (Pubitemid 47608583)
9. Chambolle A 2004 An algorithm for total variation minimization and applications J. Math. Imaging Vis. 20 8997
10. Chan T, Golub G and Mulet P 1996 A nonlinear primal-dual method for total variation-based image restoration Proc. ICAOS'96 (12th Int. Conf. Anal. and Optim. of Syst. Images) Lect. Notes Control Inf. Sci. 24152 (Pubitemid 126087819)
11. Chaudhari A J, Ahn S, Levenson R, Badawi R D, Cherry S R and Leahy R M 2009 Excitation spectroscopy in multispectral optical fluorescence tomography: methodology, feasibility and computer simulation studies Phys. Med. Biol. 54 4687704
12. Chen S S, Donoho D L and Saunders M A 1998 Atomic decomposition by basis pursuit SIAM J. Sci. Comput. 20 3361 (Pubitemid 128689501)
13. Daubechies I, Friese M D and Mol C D 2004 An iterative thresholding algorithm for linear inverse problems with a sparsity constraint Commun. Pure and Appl. Math. 57 141357 (Pubitemid 39427442)
14. Dice L 1945 Measures of the amount of ecologic association between species Ecology 26 297302
15. Dogdas B, Stout D, Chatziioannou A and Leahy R M 2007 Digimouse: a 3D whole body mouse atlas from CT and cryosection data Phys. Med. Biol. 52 57787 (Pubitemid 46646432)
16. Donoho D L 2006 Compressed sensing IEEE Trans. Inf. Theory 52 12891306
17. Dutta J 2011 Computational methods for fluorescence molecular tomography PhD Thesis University of Southern California Los Angeles, California
18. Dutta J, Ahn S, Joshi A A and Leahy R M 2009 Optimal illumination patterns for fluorescence tomography ISBI'09: Proc. IEEE Int. Symp. Biomed. Imaging: From Nano to Macro (Boston, MA, 28 June1 July 2009) pp 127578
19. Dutta J, Ahn S, Joshi A A and Leahy R M 2010 Illumination pattern optimization for fluorescence tomography: theory and simulation studies Phys. Med. Biol. 55 2961
20. Dutta J, Ahn S, Li C, Chaudhari A J, Cherry S R and Leahy R M 2008 Computationally efficient perturbative forward modeling for 3D multispectral bioluminescence and fluorescence tomography Proc. SPIE: Medical Imaging 2008 p 69130C
21. Efron B, Hastie T, Johnstone I and Tibshirani R 2004 Least angle regression Ann. Stat. 32 40799 (Pubitemid 41250302)
22. Eppstein M J, Hawrysz D J, Godavarty A and Sevick-Muraca E M 2002 Three-dimensional, Bayesian image reconstruction from sparse and noisy data sets: near-infrared fluorescence tomography Proc. Natl Acad. Sci. 99 961924 (Pubitemid 34831096)
23. Erdogan H and Fessler J A 1999 Ordered subsets algorithms for transmission tomography Phys. Med. Biol. 44 283551 (Pubitemid 29529363)
24. Fessler J A, Clinthorne N H and Rogers W L 1992 Regularized emission image reconstruction using imperfect side information IEEE Trans. Nucl. Sci. 39 146471 (Pubitemid 23608540)
25. Fessler J A and Hero A O III 1995 Penalized maximum-likelihood image reconstruction using space-alternating generalized EM algorithms IEEE Trans. Image Process. 4 141729
26. Figueiredo M A T, Nowak R D and Wright S J 2007 Gradient projection for sparse reconstruction: application to compressed sensing and other inverse problems IEEE J. Sel. Top. Signal Process. 1 58697 (Pubitemid 351276802)
27. Gao H and Zhao H 2010a Multilevel bioluminescence tomography based on radiative transfer equation: part 1: L1 regularization Opt. Express 18 185471
28. Gao H and Zhao H 2010b Multilevel bioluminescence tomography based on radiative transfer equation: part 2: Total variation and L1 data fidelity Opt. Express 18 2894912
29. Gardner C et al 2010 Improved in vivo fluorescence tomography and quantitation in small animals using a novel multiview, multispectral imaging system (Biomedical Optics, OSA Technical Digest (CD) (Optical Society of America, 2010)) OSA. Paper BTuF1 (Available at http://www.opticsinfobase.org/ abstract.cfm?URI=BIOMED-2010-BTuF1)
30. Green P J 1990 Bayesian reconstructions from emission tomography data using a modified EM algorithm IEEE Trans. Med. Imaging 9 8493
31. Guven M, Yazici B, Intes X and Chance B 2005 Diffuse optical tomography with a priori anatomical information Phys. Med. Biol. 50 2837
32. Hebert T and Leahy R M 1989 A generalized EM algorithm for 3-D Bayesian reconstruction from Poisson data using Gibbs priors IEEE Trans. Med. Imaging 8 194202
33. Huang Y, Ng M K and Wen Y W 2008 A fast total variation minimization method for image restoration Multiscale Model. Simul. 7 77495
34. Hyde D, Miller E L, Brooks D H and Ntziachristos V 2010 Data specific spatially varying regularization for multimodal fluorescence molecular tomography IEEE Trans. Med. Imaging 29 36574
35. Joshi A A, Chaudhari A J, Li C, Dutta J, Cherry S R, Shattuck D W, Toga A W and Leahy R M 2010 DigiWarp: a method for deformable mouse atlas warping to surface topographic data Phys. Med. Biol. 55 6197
36. Joshi A A, Chaudhari A J, Li C, Shattuck D, Dutta J, Leahy R M and Toga A W 2009 Posture matching and elastic registration of a mouse atlas to surface topography range data ISBI'09: Proc. IEEE Int. Symp. on Biomedical Imaging: From Nano to Macro (Boston, MA, 28 June 1 July 2009) pp 3669
37. Joshi A, Bangerth W and Sevick-Muraca E M 2006 Non-contact fluorescence optical tomography with scanning patterned illumination Opt. Express 14 651634 (Pubitemid 44036385)
38. Kim S J, Koh K, Lustig M, Boyd S and Gorinevsky D 2007 An interior-point method for large-scale l1-regularized least-squares IEEE J. Sel. Top. Signal Process. 1 60617 (Pubitemid 351266626)
39. Klose A, Ntziachristos V and Hielscher A 2005 The inverse source problem based on the radiative transfer equation in optical molecular imaging J. Comput. Phys. 202 32345 (Pubitemid 39518860)
40. Lange K 1990 Convergence of em image reconstruction algorithms with Gibbs smoothing IEEE Trans. Med. Imaging 9 43946
41. Lange K and Fessler J A 1995 Globally convergent algorithms for maximum a posteriori transmission tomography IEEE Trans. Image Process. 4 14308
42. Lange K, Hunter D R and Yang I 2000 Optimization transfer using surrogate objective functions J. Comput. Graph. Stat. 9 120
43. Leahy R M and Yan X 1991 Incorporation of anatomical MR data for improved functional imaging with PET Information Processing in Medical Imaging, Lect. Notes Comput. Sci 511 10520
44. Li A, Boverman G, Zhang Y, Brooks D, Miller E L, Kilmer M E, Zhang Q, Hillman E M C and Boas D A 2005 Optimal linear inverse solution with multiple priors in diffuse optical tomography Appl. Opt. 44 194856 (Pubitemid 40479546)
45. Li C, Mitchell G S, Dutta J, Ahn S, Leahy R M and Cherry S R 2009 A three-dimensional multispectral fluorescence optical tomography imaging system for small animals based on a conical mirror design Opt. Express 17 757185
46. Li Q, Ahn S and Leahy R M 2005 Fast hybrid algorithms for PET image reconstruction IEEE Nucl. Sci. Symp. Conf. Rec. 4 3903
47. Loening A and Gambhir S 2003 AMIDE: a free software tool for multimodality medical image analysis Mol. Imag. 2 1317
48. Massoud T F and Gambhir S S 2003 Molecular imaging in living subjects: seeing fundamental biological processes in a new light Genes Dev. 17 54580 (Pubitemid 36307540)
49. Mohajerani P, Eftekhar A A, Huang J and Adibi A 2007 Optimal sparse solution for fluorescent diffuse optical tomography: theory and phantom experimental results Appl. Opt. 46 167985 (Pubitemid 46659534)
50. Natarajan B K 1995 Sparse approximate solutions to linear systems SIAM J. Comput. 24 22734
51. Pogue B W, McBride T O, Prewitt J, sterberg U L and Paulsen K D 1999 Spatially variant regularization improves diffuse optical tomography Appl. Opt. 38 295061 (Pubitemid 129598418)
52. Rudin L I, Osher S and Fatemi E 1992 Nonlinear total variation based noise removal algorithms Phys. D: Nonlinear Phenom. 60 25968
53. Shu X, Royant A, Lin M Z, Aguilera T A, Lev-Ram V, Steinbach P A and Tsien R Y 2009 Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome Science 324 8047
54. Stout D, Chow P, Silverman R, Leahy R M, Lewis X, Gambhir S and Chatziioannou A 2002 Creating a whole body digital mouse atlas with PET, CT and cryosection images Mol. Imag. Biol. 4 S27
55. Strong D and Chan T 2003 Edge-preserving and scale-dependent properties of total variation regularization Inverse Problems 19 S165
56. Tibshirani R 1996 Regression shrinkage and selection via the Lasso J. R. Stat. Soc. B 58 26788 (Available at http://www.jstor.org/pss/2346178)
57. Tikhonov A N and Arsenin V Y 1977 Solutions of Ill-Posed Problems (Washington, DC: Wiley)
58. Vogel C and Oman M 1996 Iterative methods for total variation denoising SIAM J. Sci. Comput. 17 22738 (Pubitemid 126621162)
59. Vogel C R and Oman M E 1998 Fast, robust total variation-based reconstruction of noisy, blurred images IEEE Trans. Image Process. 7 81324 (Pubitemid 128745393)
60. Weissleder R and Ntziachristos V 2003 Shedding light onto live molecular targets Nature Med. 9 1238 (Pubitemid 36098273)
61. Weissleder R, Tung C H, Mahmood U and Bogdanov A 1999 In vivo imaging of tumors with protease-activated near-infrared fluorescent probes Nature Biotechnol. 17 3758 (Pubitemid 29166041)
62. Zacharakis G, Kambara H, Shih H, Ripoll J, Grimm J, Saeki Y, Weissleder R and Ntziachristos V 2005 Volumetric tomography of fluorescent proteins through small animals in vivo Proc. Natl Acad. Sci. 102 182527 (Pubitemid 43011213)