Medical Image Analysis
Volume 14, Issue 6 , Pages 723-737 , December 2010

Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data

  • Martin Baiker

      Affiliations

    • Div. of Image Processing, Leiden University Medical Center, 2300 Leiden, The Netherlands
    • Corresponding Author InformationCorresponding author. Tel.: +31 715261117; fax: +31 715266801.
    • ,
  • Julien Milles

      Affiliations

    • Div. of Image Processing, Leiden University Medical Center, 2300 Leiden, The Netherlands
    • ,
  • Jouke Dijkstra

      Affiliations

    • Div. of Image Processing, Leiden University Medical Center, 2300 Leiden, The Netherlands
    • ,
  • Tobias D. Henning

      Affiliations

    • University of California, San Francisco, USA
    • ,
  • Axel W. Weber

      Affiliations

    • Dept. of Nuclear Medicine, TU München, Munich, Germany
    • ,
  • Ivo Que

      Affiliations

    • Dept. of Endocrinology, Leiden University Medical Center, 2300 Leiden, The Netherlands
    • ,
  • Eric L. Kaijzel

      Affiliations

    • Dept. of Endocrinology, Leiden University Medical Center, 2300 Leiden, The Netherlands
    • ,
  • Clemens W.G.M. Löwik

      Affiliations

    • Dept. of Endocrinology, Leiden University Medical Center, 2300 Leiden, The Netherlands
    • ,
  • Johan H.C. Reiber

      Affiliations

    • Div. of Image Processing, Leiden University Medical Center, 2300 Leiden, The Netherlands
    • ,
  • Boudewijn P.F. Lelieveldt

      Affiliations

    • Div. of Image Processing, Leiden University Medical Center, 2300 Leiden, The Netherlands
    • Dept. of Mediamatics, Delft University of Technology, Delft, The Netherlands
    • Corresponding Author InformationCorresponding author at: Div. of Image Processing, Leiden University Medical Center, 2300 Leiden, The Netherlands.
    web address

Received 10 September 2009 ,Revised 26 February 2010 ,Accepted 26 April 2010.

References 

  1. Alexandrakis G, Rannou FR, Chatziioannou AF. Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study. Physics in Medicine and Biology. 2005;50(17):4225–4241
  2. Alexandrakis G, Rannou F, Chatziioannou A. Effect of optical property estimation accuracy on tomographic bioluminescence imaging: simulation of a combined optical pet (opet) system. Physics in Medicine and Biology. 2006;51:2045–2053
  3. Arsigny V, Commowick O, Ayache N, Pennec X. A fast and log-euclidean polyaffine framework for locally linear registration. Journal of Mathematical Imaging and Vision. 2009;33(2):222–238
  4. Bab I, Hajbi-Yonissi C, Gabet Y, Müller R. Micro-Tomographic Atlas of the Mouse Skeleton. NY, USA: Springer; 2007;ISBN-13: 978-0-387-39254-7
  5. Baiker, M., Milles, J., Vossepoel, A.M., Que, I., Kaijzel, E.L., Löwik, C.W.G.M., Reiber, J.H.C., Dijkstra, J., Lelieveldt, B.P.F., 2007. Fully automated whole-body registration in mice using an articulated skeleton atlas. In: Proceedings of the IEEE International Symposium on Biomedical Imaging, pp. 728–731.
  6. Baiker, M., Dijkstra, J., Que, I., Löwik, C.W.G.M., Reiber, J.H.C., Lelieveldt, B.P.F., 2008. Organ approximation in μCT data with low soft tissue contrast using an articulated whole-body atlas. In: Proceedings of the IEEE International Symposium on Biomedical Imaging, pp. 1267–1270.
  7. Belongie S, Malik J, Puzicha J. Shape matching and object recognition using shape contexts. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2002;24(4):509–522
  8. Besl PJ, McKay ND. A method for registration of 3D shapes. IEEE Transactions on Pattern Analysis and Machine Intelligence. 1992;14(2):239–256
  9. Bookstein FL. Principal warps – Thin-Plate-Splines and the decomposition of deformations. IEEE Transactions on Pattern Analysis and Machine Intelligence. 1989;11(6):567–585
  10. Chaudhari, A.J., Joshi, A.A., Darvas, F., Leahy, R.M., 2007. A method for atlas-based volumetric registration with surface constraints for optical bioluminescence tomography in small animal imaging. In: Proceedings of the SPIE Medical Imaging, vol. 6510, pp. 651024-1–651024-10.
  11. Cheers G. Anatomica. Weltbild Verlag; 2004;ISBN-10: 3828920683
  12. Chui H, Rangarajan A. A new point matching algorithm for non-rigid registration. Computer Vision and Image Understanding. 2003;89(3):114–141
  13. Coleman T, Li Y. An interior, trust region approach for nonlinear minimization subject to bounds. SIAM Journal on Optimization. 1996;6(5):418–445
  14. Commowick O, Arsigny V, Isambert A, Costa J, Dhermain F, Bidault F, et al. An efficient locally affine framework for the smooth registration of anatomical structures. Medical Image Analysis. 2008;12(4):427–441
  15. Cook MJ. Anatomy of the Laboratory Mouse. San Diego, US: Academic Press Inc.; 1965;ISBN-13: 978-0121869502
  16. Dice L. Measures of the amount of ecologic association between species. Ecology. 1945;297–302
  17. Dogdas B, Stout D, Chatziioannou AF, Leahy RM. Digimouse: a 3D whole body mouse atlas from CT and cryosection data. Physics in Medicine and Biology. 2007;52(3):577–587
  18. du Bois d’Aische, A., De Craene, M., Macq, B., Warfield, S.K., 2005. An articulated registration method. In: Proceedings of the IEEE International Conference on Image Processing, vol. 1, pp. 21–24.
  19. Elad A, Kimmel R. On bending invariant signatures for surfaces. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2003;25(10):1285–1295
  20. Garland M, Shaffer E. A multiphase approach to efficient surface simplification. In: VIS ’02: Proceedings of the Conference on Visualization ’02. Washington, DC, USA: IEEE Computer Society; 2002;p. 117–124
  21. Gatzke, T., Grimm, C., 2005. Curvature maps for local shape comparison. In: Shape Modeling International, pp. 244–256.
  22. Henning T, Weber AW, Bauer JS, Meier R, Carlsen JM, Sutton EJ, et al. Imaging characteristics of DHOG, a hepatobiliary contrast agent for preclinical microCT in mice. Academic Radiology. 2008;15(3):342–349
  23. Hill DLG, Batchelor PG, Holden M, Hawkes DJ. Medical image registration. Physics in Medicine and Biology. 2001;46(3):R1–R45
  24. Holden M. A review of geometric transformations for nonrigid body registration. IEEE Transactions on Medical Imaging. 2008;27(1):111–128
  25. Jain V, Zhang H. A spectral approach to shape-based retrieval of articulated 3d models. Computer-Aided Design. 2007;39(5):398–407
  26. Kaijzel E, van der Pluijm G, Löwik C. Whole-body optical imaging in animal models to assess cancer development and progression. Clinical Cancer Research. 2007;13(12):3490
  27. Kaijzel E, Snoeks T, Buijs J, van der Pluijm G, Löwik C. Multimodal imaging and treatment of bone metastasis. Clinical and Experimental Metastasis. 2009;26(4):371–379
  28. Kimmel R, Sethian JA. Computing geodesic paths on manifolds. Proceedings of National Academy of Sciences. 1998;95(15):8431–8435
  29. Kok, P., Dijkstra, J., Botha, C.P., Post, F.H., Kaijzel, E., Que, I., Löwik, C.W.G.M., Reiber, J.H.C., Lelieveldt, B.P.F., 2007. Integrated visualization of multi-angle bioluminescence imaging and micro CT. In: Proceedings of the SPIE Medical Imaging, vol. 6509, pp. 1–10.
  30. Kovacevic, N., Hamarneh, G., Henkelman, M., 2003. Anatomically guided registration of whole body mouse MR images. In: Proceedings of the MICCAI, pp. 870–877.
  31. Krücker JF, LeCarpentier GL, Fowlkes JB, Carson PL. Rapid elastic image registration for 3-D ultrasound. IEEE Transactions on Medical Imaging. 2002;21(11):1384–1394
  32. Li X, Yankeelov TE, Peterson TE, Gore JC, Dawant BM. Automatic nonrigid registration of whole body ct mice images. Medical Physics. 2008;35(4):1507–1520
  33. Lorensen, W.E., Cline, H.E., 1987. Marching cubes: a high resolution 3d surface construction algorithm. In: SIGGRAPH ’87: Proceedings of the 14th Annual Conference on Computer Graphics and Interactive Techniques, pp. 163–169.
  34. Maintz JBA, Viergever MA. A survey of medical image registration. Medical Image Analysis. 1998;2(1):1–36
  35. Martín-Fernández, M.A., Munoz Moreno, E., Martín-Fernández, M., Alberola-López, C., 2005. Articulated registration: elastic registration based on a wire model. In: Proceedings of the SPIE Medical Imaging, vol. 5747, pp. 182–191.
  36. Martín-Fernández, M.A., Cárdenes, R., Munoz Moreno, E., de Luis-García, R., Martín-Fernández, M., Alberola-López, C., in press. Automated articulated registration of hand radiographs. Image and Vision Computing.
  37. Massoud TF, Gambhir SS. Molecular imaging in living subjects: seeing fundamental biological processes in a new light. Genes and Development. 2003;17(5):545–580
  38. Papademetris, X., Dione, D.P., Dobrucki, L.W., Staib, L., Sinusas, A.J., 2005. Articulated rigid registration for serial lower-limb mouse imaging. In: Proceedings of the MICCAI, pp. 919–926.
  39. Pearson K. On lines and planes of closest fit to systems of points in space. Philosophical Magazine. 1901;2(6):559–572
  40. Pluim JPW, Maintz JBA, Viergever MA. Mutual-information-based registration of medical images: a survey. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2003;22(8):986–1004
  41. Ridler TW, Calvard S. Picture thresholding using an iterative selection method. IEEE Transactions on Systems, Man, and Cybernetics. 1978;8(8):630–632
  42. Rohlfing T, Maurer C, Bluemke D, Jacobs M. Volume-preserving nonrigid registration of MR breast images using free-form deformation with an incompressibility constraint. IEEE Transactions on Medical Imaging. 2003;22(6):730–741
  43. Rohr K, Stiehl HS, Sprengel R, Buzug TM, Weese J, Kuhn MH. Landmark-based elastic registration using approximating Thin-Plate-Splines. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2001;20(6):526–534
  44. Segars WP, Tsui BMW, Frey EC, Johnson GA, Berr SS. Development of a 4D digital mouse phantom for molecular imaging research. Molecular Imaging and Biology. 2004;6(3):149–159
  45. Soutiere S, Tankersley C, Mitzner W. Differences in alveolar size in inbred mouse strains. Respiratory Physiology & Neurobiology. 2004;140(3):283–291
  46. Sumner RW, Popović J. Deformation transfer for triangle meshes. In: SIGGRAPH ’04: ACM SIGGRAPH 2004 Papers. New York, NY, USA: ACM Press; 2004;p. 399–405
  47. Wahba G. Spline Models for Observational Data. Philadelphia: SIAM; 1990;
  48. Walimbe V, Shekhar R. Automatic elastic image registration by interpolation of 3d rotations and translations from discrete rigid-body transformations. Medical Image Analysis. 2006;10(6):899–914
  49. Wang YM, Peterson BS, Staib LH. 3D brain surface matching based on geodesics and local geometry. Computer Vision and Image Understanding. 2003;89(2–3):252–271
  50. Weissleder R, Mahmood U. Molecular imaging. Radiology. 2001;219(2):316–333
  51. Zack GW, Rogers WE, Latt SA. Automatic measurement of sister chromatid exchange frequency. Journal of Histochemistry and Cytochemistry. 1977;25(7):741–753
  52. Zayer R, Rössl C, Karni Z, Seidel H-P. Harmonic guidance for surface deformation. In:  Alexa M,  Marks J editor. The European Association for Computer Graphics 26th Annual Conference: EUROGRAPHICS 2005, Computer Graphics Forum, Eurographics. vol. 24:Dublin, Ireland: Blackwell; 2005;p. 601–609
  53. Zhang X, Badea C, Johnson G. Three-dimensional reconstruction in free-space whole-body fluorescence tomography of mice using optically reconstructed surface and atlas anatomy. Journal of Biomedical Optics. 2009;14:064010
  54. Zitova B, Flusser J. Image registration methods: a survey. Image and Vision Computing. 2003;21(11):977–1000

PII: S1361-8415(10)00044-7

doi: 10.1016/j.media.2010.04.008

Medical Image Analysis
Volume 14, Issue 6 , Pages 723-737 , December 2010

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