Estimation of mouse organ locations through registration of a statistical mouse atlas with micro-CT images

IEEE Transactions on Medical Imaging

Volumn 31, Issue 1, 2012, Pages 88-102

  Wang, Hongkai ^a   Stout, David B ^a   Chatziioannou, Arion F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Atlas registration; conditional Gaussian model; micro CT; mouse atlas; statistical shape model

Indexed keywords

ATLAS REGISTRATION; CONDITIONAL GAUSSIAN MODEL; MICRO-CT; MOUSE ATLAS; STATISTICAL SHAPE MODEL;

ESTIMATION; GAUSSIAN DISTRIBUTION; IMAGE SEGMENTATION; MAMMALS; STATISTICS; TISSUE;

COMPUTERIZED TOMOGRAPHY;

ANIMAL; ARTICLE; BONE; C57BL MOUSE; FEMALE; HEART; HISTOLOGY; IMAGE PROCESSING; KIDNEY; LIVER; LUNG; MALE; METHODOLOGY; MICRO-COMPUTED TOMOGRAPHY; MOUSE; MOUSE MUTANT; NUDE MOUSE; PRINCIPAL COMPONENT ANALYSIS; RADIOGRAPHY; SPLEEN; WHOLE BODY IMAGING;

ANIMALS; BONE AND BONES; FEMALE; HEART; IMAGE PROCESSING, COMPUTER-ASSISTED; KIDNEY; LIVER; LUNG; MALE; MICE; MICE, INBRED C57BL; MICE, NUDE; MICE, SCID; PRINCIPAL COMPONENT ANALYSIS; SPLEEN; WHOLE BODY IMAGING; X-RAY MICROTOMOGRAPHY;

EID: 84855363809     PISSN: 02780062     EISSN: None     Source Type: Journal    
DOI: 10.1109/TMI.2011.2165294     Document Type: Article

References (65)

1. H. Li, H. Zhang, Z. Tang, and G. Hu, "Micro-computed tomography for small animal imaging: Technological details," Prog. Nat. Sci., vol. 18, pp. 513-521, May 2008.
2. P. L. Chow, D. B. Stout, E. Komisopoulou, and A. F. Chatziioannou, "A method of image registration for small animal, multi-modality imaging," Phys. Med. Biol., vol. 51, pp. 379-390, Jan. 2006. (Pubitemid 43231978)
3. B. L. Franc, P. D. Acton, C.Mari, and B. H. Hasegawa, "Small-animal SPECT and SPECT/CT: Important tools for preclinical investigation," J. Nucl. Med., vol. 49, pp. 1651-1663, Oct. 2008.
4. R. B. Schulz, A. Ale, A. Sarantopoulos, M. Freyer, E. Soehngen, M. Zientkowska, and V. Ntziachristos, "Hybrid system for simultaneous fluorescence and X-ray computed tomography," IEEE Trans. Med. Imag., vol. 29, no. 2, pp. 465-473, Feb. 2010.
5. X. Guo, X. Liu, X. Wang, F. Tian, F. Liu, B. Zhang, G. Hu, and J. Bai, "A combined fluorescence and microcomputed tomography system for small animal imaging," IEEE Trans. Biomed. Eng., vol. 57, no. 12, pp. 2876-2883, Dec. 2010.
6. Y. W. J. Liu, 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, vol. 18, pp. 13102-13113, 2010.
7. C. G. Radu, C. J. Shu, E. Nair-Gill, S.M. Shelly, J. R. Barrio, N. Satyamurthy, M. E. Phelps, and O. N. Witte, "Molecular imaging of lymphoid organs and immune activation by positron emission tomography with a new [18F]-labeled 2'-deoxycytidine analog," Nat. Med., vol. 14, pp. 783-788, Jul. 2008. (Pubitemid 351951515)
8. E. L. Ritman, "Micro-computed tomography of the lungs and pulmonary-vascular system," in Proc. Am. Thorac. Soc., Dec. 2005, vol. 2, pp. 477-480. (Pubitemid 43128017)
9. J. C. Garrison, T. L. Rold, G. L. Sieckman, S. D. Figueroa, W. A. Volkert, S. S. Jurisson, and T. J. Hoffman, "In vivo evaluation and small-animal PET/CT of a prostate cancer mouse model using 64Cu bombesin analogs: Side-by-side comparison of the CB-TE2A and DOTA chelation systems," J. Nucl. Med., vol. 48, pp. 1327-1337, Aug. 2007. (Pubitemid 47242799)
10. N. L. Ford, M. M. Thornton, and D. W. Holdsworth, "Fundamental image quality limits for microcomputed tomography in small animals," Med. Phys., vol. 30, pp. 2869-2877, Nov. 2003. (Pubitemid 37444296)
11. I. Willekens, T. Lahoutte, N. Buls, C. Vanhove, R. Deklerck, A. Bossuyt, and J. de Mey, "Time-course of contrast enhancement in spleen and liver with Exia 160, Fenestra LC, and VC," Mol. Imag. Biol., vol. 11, pp. 128-135, 2009.
12. M. Baiker, B. Vastenhouw, W. Branderhorst, J. H. C. Reiber, F. Beekman, and B. P. F. Lelieveldt, "Atlas-driven scan planning for high-resolution micro-SPECT data acquisition based on multi-view photographs: A pilot study," in Proc. SPIE Medical Imaging 2009: Visualization, Image-Guided Procedures, and Modeling, M. I. Miga and K. H. Wong, Eds., 2009, pp. 72611L-8.
13. M.H.Wildeman, M. Baiker, J.H.C.Reiber, C. W. G. M. Lowik, M. J. T. Reinders, and B. P. F. Lelieveldt, "2D/3D registration of micro-CT data to multi-view photographs based on a 3D distance map," in Proc. 6th IEEE Int. Symp. Biomed. Imag.: FromNano toMacro, Boston, MA, USA, 2009, pp. 987-990.
14. 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," in Proc. SPIE Medical Imaging 2007: Physics ofMedical Imaging, J. Hsieh and M. J. Flynn, Eds., 2007, pp. 651024-10.
15. A. A. Joshi, A. J. Chaudhari, C. Li, J. Dutta, S. R. Cherry, D.W. Shattuck, A. W. Toga, and R. M. Leahy, "DigiWarp: A method for deformable mouse atlas warping to surface topographic data," Phys.Med. Biol., vol. 55, pp. 6197-6214, Oct. 2010.
16. M. Baiker, J. Milles, J. Dijkstra, T. D. Henning, A. W. Weber, I. Que, E. L. Kaijzel, C. W. Lowik, J. H. Reiber, and B. P. Lelieveldt, "Atlasbased whole-body segmentation of mice from low-contrast micro-CT data," Med. Image Anal., vol. 14, pp. 723-737, 2010.
17. 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," in Proc. SPIE Medical Imaging 2011: Biomedical Applications in Molecular, Structural, and Functional Imaging, 2011, pp. 79650E-7.
18. S. Somayajula, A. A. Joshi, and R. M. Leahy, "Mutual information based non-rigidmouse registration using a scale-space approach," in Proc. IEEE Int. Symp. Biomed. Imag., 2008, pp. 1147-1150.
19. X. Li, T. E. Yankeelov, T. E. Peterson, J. C. Gore, and B.M. Dawant, "Automatic nonrigid registration of whole body CT mice images," Med. Phys., vol. 35, pp. 1507-1520, Apr. 2008. (Pubitemid 351457519)
20. N. Kovacevic, G. Hamarneh, and M. Henkelman, "Anatomically guided registration of whole body mouse MR images," in Proc. Medical Image Computing and Computer-Assisted Intervention (MICCAI 2003), R. E. Ellis and T. M. Peters, Eds., 2003, pp. 870-877.
21. H. Park, P. H. Bland, and C. R. Meyer, "Construction of an abdominal probabilistic atlas and its application in segmentation," IEEE Trans. Med. Imag., vol. 22, no. 4, pp. 483-492, Apr. 2003.
22. I. Isgum, M. Staring, A. Rutten, M. Prokop, M. A. Viergever, and B. van Ginneken, "Multi-atlas-based segmentation with local decision fusion-application to cardiac and aortic segmentation in CT scans," IEEE Trans. Med. Imag., vol. 28, no. 7, pp. 1000-1010, Jul. 2009.
23. H. Ólafsdóttir, M. Hansen, K. Sjöstrand, T. Darvann, N. Hermann, E. Oubel, B. Ersbøll, R. Larsen, A. Frangi, P. Larsen, C. Perlyn, G.Morriss-Kay, and S. Kreiborg, "Sparse statistical deformationmodel for the analysis of craniofacial malformations in the crouzon mouse," in Proc. Scandinavian Confe. Image Anal. (SCIA 2007), B. K. Ersbøll and K. S. Pedersen, Eds., 2007, pp. 112-121.
24. N. Kovacevic, J. T. Henderson, E. Chan, N. Lifshitz, J. Bishop, A. C. Evans, R. M. Henkelman, and X. J. Chen, "A three-dimensional MRI atlas of the mouse brain with estimates of the average and variability," Cereb. Cortex, vol. 15, pp. 639-645, May 2005. (Pubitemid 40577479)
25. C. Barillot, D. R. Haynor, P. Hellier, H. Okuda, P. Shkarin, K. Behar, J. S. Duncan, and X. Papademetris, "Construction of a 3D volumetric probabilistic model of the mouse kidney from MRI," in Proc. Medical Image Computing and Computer-Assisted Intervention (MICCAI 2004), 2004, pp. 1052-1054. (Pubitemid 40787335)
26. A. L. Kesner, M. Dahlbom, S. C. Huang, W. A. Hsueh, B. S. Pio, J. Czernin, M. Kreissl, H. M. Wu, and D. H. S. Silverman, "Semiautomated analysis of small-animal PET data," J. Nucl. Med., vol. 47, pp. 1181-1186, Jul. 2006. (Pubitemid 47544913)
27. R. Maroy, R. Boisgard, C. Comtat, B. Jego, Y. Fontyn, S. Jan, A. Dubois, R. Trebossen, and B. Tavitian, "Quantitative organ time activity curve extraction from rodent PET images without anatomical prior," Med. Phys., vol. 37, pp. 1507-1517, Apr. 2010.
28. T. Heimann and H. P. Meinzer, "Statistical shape models for 3D medical image segmentation: A review," Med. Image Anal., vol. 13, pp. 543-563, Aug. 2009.
29. J. E. Iglesias and M. de Bruijne, "Semiautomatic segmentation of vertebrae in lateral X-rays using a conditional shapemodel," Acad. Radiol., vol. 14, pp. 1156-1165, Oct. 2007. (Pubitemid 47418685)
30. C. Suckow and D. Stout, "MicroCT liver contrast agent enhancement over time, dose, and mouse strain," Mol. Imag. Biol., vol. 10, pp. 114-120, 2008.
31. C. Suckow, C. Kuntner, P. Chow, R. Silverman, A. Chatziioannou, and D. Stout, "Multimodality rodent imaging chambers for use under barrier conditions with gas anesthesia," Mol. Imag. Biol., vol. 11, pp. 100-106, 2009.
32. H. Delingette, "General object reconstruction based on simplex meshes," Int. J. Comput. Vis., vol. 32, pp. 111-146, 1999.
33. P. Kohli and P. H. S. Torr, "Efficiently solving dynamic Markov random fields using graph cuts," in Proc. IEEE Int. Conf. Comput. Vis. (ICCV 05), 2005, pp. 922-929. (Pubitemid 44042280)
34. Y. Boykov and V. Kolmogorov, "An experimental comparison of mincut/max-flow algorithms for energy minimization in vision," IEEE Trans. Pattern Anal. Mach. Intell., vol. 26, no. 9, pp. 1124-1137, Sep. 2004.
35. E. L.William and E. C. Harvey, "Marching cubes:Ahigh resolution 3D surface construction algorithm," in Proc. Comput. Graphics Interactive Techn. (SIGGRAPH 87), 1987, pp. 163-169.
36. G. Michael and S. H. Paul, "Surface simplification using quadric error metrics," in Proc. Comput. Graphics Interactive Tech. (SIGGRAPH 97), 1997, pp. 209-216.
37. J. Bing and B. C. Vemuri, "A robust algorithm for point set registration using mixture of Gaussians," in Proc. IEEE Int. Conf. Comput. Vis. (ICCV 2005), 2005, pp. 1246-1251.
38. F. L. Bookstein, "Shape and the information in medical images: A decade of the morphometric synthesis," Comput. Vis. Image Understand., vol. 66, pp. 97-118, 1997. (Pubitemid 127435275)
39. M. Bosc, F. Heitz, and J.-P. Armspach, "Statistical atlas-based subvoxel segmentation of 3D brain MRI," in Proc. IEEE Int. Conf. Image Process. (ICIP 03), Sep. 2003, p. 1077.
40. A. Neumann and C. Lorenz, "Statistical shape model based segmentation of medical images," Comput. Med. Imag. Graph., vol. 22, pp. 133-143, Mar.-Apr. 1998. (Pubitemid 28400202)
41. F. L. Bookstein, "Landmarkmethods for forms without landmarks: Localizing group differences in outline shape," in Proc. Math. Methods in Biomed. Image Anal. (MMBIA 19 ), 1996, pp. 279-289.
42. H. Hotelling, "Analysis of a complex of statistical variables into principal components," J. Educ. Psychol., vol. 24, pp. 498-520, 1933.
43. "Thresholding using the ISODATA clustering algorithm," IEEE Trans. Syst. Man Cybern., vol. 10, no. 11, pp. 771-774, Nov. 1980.
44. H. L. Chui and A. Rangarajan, "A new point matching algorithm for non-rigid registration," Comput. Vis. Image Understand., vol. 89, pp. 114-141, Feb.-Mar. 2003.
45. M. Lorenzo-Valdes, G. I. Sanchez-Ortiz, A. G. Elkington, R. H. Mohiaddin, and D. Rueckert, "Segmentation of 4D cardiacMRimages using a probabilistic atlas and the EM algorithm," Med. Image Anal., vol. 8, pp. 255-265, Sep. 2004. (Pubitemid 39185909)
46. C. Casteels, P. Vermaelen, J. Nuyts, A. Van Der Linden, V. Baekelandt, L. Mortelmans, G. Bormans, and K. Van Laere, "Construction and evaluation of multitracer small-animal PET probabilistic atlases for voxel-based functional mapping of the rat brain," J. Nucl. Med., vol. 47, pp. 1858-1866, Nov. 2006. (Pubitemid 47545009)
47. D. Stout, A. Chatziioannou, T. Lawson, R. Silverman, S. Gambhir, and M. Phelps, "Small animal imaging center design: The facility at the UCLA Crump Institute for Molecular Imaging," Mol. Imag. Biol., vol. 7, pp. 393-402, 2005. (Pubitemid 44193404)
48. W. P. Segars,B. M.W. Tsui, E.C. Frey, G. A. Johnson, and S. S. Berr, "Development of a 4-D digital mouse phantom for molecular imaging research," Mol. Imag. Biol., vol. 6, pp. 149-159, May-Jun. 2004. (Pubitemid 38771978)
49. 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., vol. 52, pp. 577-587, Feb. 2007. (Pubitemid 46646432)
50. D. Stout, P. Chow, R. Silverman, R. M. Leahy, X. Lewis, S. Gambhir, and A. Chatziioannou, "Creating a whole body digital mouse atlas with PET, CT and cryosection images," Mol. Imag. Biol., vol. 4, p. S27, 2002.
51. J. Koikkalainen, T. Tolli, K. Lauerma, K. Antila, E. Mattila, M. Lilja, and J. Lotjonen, "Methods of artificial enlargement of the training set for statistical shape models," IEEE Trans. Med. Imag., vol. 27, no. 11, pp. 1643-1654, Nov. 2008.
52. C. T. Badea, A. W.Wetzel,N.Mistry, S. Pomerantz, D.Nave, and G. A. Johnson, "Left ventricle volume measurements in cardiac micro-CT: The impact of radiation dose and contrast agent," Comput. Med. Imag. Graph., vol. 32, pp. 239-250, Apr. 2008.
53. B. Driehuys, J. Nouls, A. Badea, E. Bucholz, K. Ghaghada, A. Petiet, and L. W. Hedlund, "Small animal imaging with magnetic resonance microscopy," Ilar J., vol. 49, pp. 35-53, 2008.
54. K. Gorczowski, M. Styner, J. Y. Jeong, J. S. Marron, J. Piven, H. C. Hazlett, S. M. Pizer, and G. Gerig, "Multi-object analysis of volume, pose, and shape using statistical discrimination," IEEE Trans. Pattern Anal. Mach. Intell., vol. 32, no. 4, pp. 652-661, Apr. 2010.
55. A. Tsai, W. Wells, C. Tempany, E. Grimson, and A. Willsky, "Mutual information in coupled multi-shape model for medical image segmentation," Med. Image Anal., vol. 8, pp. 429-445, Dec. 2004. (Pubitemid 39618469)
56. T. Okada, K. Yokota, M. Hori, M. Nakamoto, H. Nakamura, and Y. Sato, "Construction of hierarchical multi-organ statistical atlases and their application to multi-organ segmentation from CT images," in Proc. Medical Image Computing and Computer-Assisted Intervention (MICCAI 2008), D. Metaxas, L. Axel, G. Fichtinger, and G. Székely, Eds., 2008, pp. 502-509.
57. A. Khmelinskii, M. Baiker, E. L. Kaijzel, J. Chen, J. H. Reiber, and B. P. Lelieveldt, "Articulated whole-body atlases for small animal image analysis: Construction and applications," Mol. Imag. Biol., vol. 13, pp. 898-910, 2011.
58. D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, C. Wimberley, M. C. Gregoire, and O. Salvado, "An accurate 3D shape context based non-rigid registration method for mouse whole-body skeleton registration," in Proc. SPIE Medical Imaging 2011: Image Processing, B. M. Dawant and D. R. Haynor, Eds., 2011, pp. 79620V-10.
59. D. Xiao, D. Zahra, P. Bourgeat, P. Berghofer, O. A. Tamayo, C. Wimberley, M. C. Gregoire, and O. Salvado, "An improved 3D shape context based non-rigid registration method and its application to small animal skeletons registration," Comput. Med. Imag. Graph., vol. 34, pp. 321-332, June 2010.
60. M. G. Linguraru, J. K. Sandberg, Z. X. Li, F. Shah, and R. M. Summers, "Automated segmentation and quantification of liver and spleen from CT images using normalized probabilistic atlases and enhancement estimation," Med. Phys., vol. 37, pp. 771-783, Feb. 2010.
61. X. R. Zhou, T. Kitagawa, T. Hara, H. Fujita, X. J. Zhang, R. Yokoyama, H. Kondo, M. Kanematsu, and H. Hoshi, "Constructing a probabilistic model for automated liver region segmentation using non-contrast X-ray torso CT images," in Proc. Med. Image Computing Computer-Assisted Intervent. (MICCAI 2006), Pt 2, 2006, pp. 856-863. (Pubitemid 44609301)
62. T. Okada, R. Shimada, M. Hori, M. Nakamoto, Y. W. Chen, H. Nakamura, and Y. Sato, "Automated segmentation of the liver from 3D CT images using probabilistic atlas andmultilevel statistical shapemodel," Acad. Radiol., vol. 15, pp. 1390-1403, Nov. 2008.
63. T. Okada, K. Yokota, M. Hori, M. Nakamoto, H. Nakamura, and Y. Sato, "Construction of hierarchical multi-organ statistical atlases and their application to multi-organ segmentation from CT images," in Proc. Med. Image Comput. Computer-Assist. Intervent. (MICCAI 2008), 2008, pp. 502-509.
64. A. Shimizu, T. Kimoto, H. Kobatake, S. Nawano, and K. Shinozaki, "Automated pancreas segmentation from three-dimensional contrast-enhanced computed tomography," Int. J. CARS, vol. 5, pp. 85-98, 2010.
65. X. Liu, M. Linguraru, J. Yao, and R. Summers, "Organ pose distribution model and an MAP framework for automated abdominal multiorgan localization," in Proc. Medical Imaging and Augmented Reality (MIAR 2010), H. Liao, P. Edwards, X. Pan, Y. Fan, and G.-Z. Yang, Eds., 2010, pp. 393-402.