Articulated Atlases Download

6 August 2010

Introduction

Using 3 publicly available anatomical whole-body atlases, Sprague-Dawley (SD) rat (Bai et al. 2006), MOBY mouse (Segars et al. 2004) and Digimouse (Dogdas et al. 2007), articulated versions of these atlases were built. To this end, major bones/bone groups were manually segmented for each atlas skeleton. Then, a kinematic model for each atlas was built: each joint position was identified and the corresponding Degrees of Freedom (DoFs) were specified, according to the joint type i.e., ball or hinge joint.

Within our research, the articulated MOBY atlas proved to be a very useful tool for whole-body segmentation of mice from low-contrast microCT (Baiker et al. 2010a, Khmelinskii and Baiker et al. 2010), multi-modality image combination (Wildeman et al. 2009, Khmelinskii et al. 2010) and follow-up studies (Baiker et al. 2010b) and proved to be a valuable tool for pre-clinical research.

For further information and details about articulated atlas construction and applications please refer to the following articles:

  • A. Khmelinskii and M. Baiker, E. L. Kaijzel, J. Chen, J. H. C. Reiber and B. P. F. Lelieveldt. Articulated whole-body atlases for small animal image analysis: construction & applications. Mol. Imaging Biol, 2010, in press, (Khmelinskii and Baiker et al. 2010)
  • M. Baiker, J. Milles, J. Dijkstra, T. Henning, A. W. Weber, I. Que, E. Kaijzel, C. W. G. M. Löwik, J. H. C. Reiber and B. P. F Lelieveldt. Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data. Med. Image Anal., 2010,in press (Baiker et al. 2010a)
  • M. Baiker, J. Dijkstra, J. Milles, C. W. G. M. Löwik, B. P. F. Lelieveldt, Paragios, N.; Duncan, J. & Ayache, N. (ed.). Handbook of Biomedical Imaging, “Atlas-based whole-body registration in mice”. Springer, N.Y., USA, 2010, in press (Baiker et al. 2010b)
  • A. Khmelinskii, M. Baiker, X. J. Chen, J. H. C. Reiber, R. M. Henkelman, and B. P. F. Lelieveldt. Atlas-based organ & bone approximation for ex-vivo µMRI mouse data: a pilot study. IEEE Intl. Symp. on Biomedical Imaging. in press, 2010(Khmelinskii et al. 2010)
  • M. H. Wildeman, M. Baiker, J. H. C. Reiber, C. W. G. M. Löwik, M. J. T. Reinders & B. P. F. Lelieveldt. 2D/3D registration of micro-CT data to multi-view photographs based on a 3D distance map. Proc. IEEE Intl. Symp. on Biomedical Imaging,2009, 987-990 (Wildeman et al. 2009)
  • M. Baiker, J. Milles, A. M. Vossepoel, I. Que, E. L. Kaijzel, C. W. G. M. Löwik, J. H. C. Reiber, J. Dijkstra & B. P. F. Lelieveldt. Fully automated whole-body registration in mice using an articulated skeleton atlas. Proc. IEEE Intl. Symp. on Biomedical Imaging, 2007, 728-731 (Baiker et al. 2007)

Acknowledgement and citation

The presented modifications to the original atlases (the manually partitioned skeletons) are free for download for academic purposes. To this end, the online form has to be filled and subsequently the download page will be loaded.
The e-mail address will be used only for verification purposes. Also, please note that we do not provide access to the original atlases; the conditions of use for the MOBY, Digimouse, and SD Rat atlases vary, and are listed on the original atlas websites. We request that any publication using one of the articulated atlases cites either the reference [1] or [2] from the list above, along with the citation requested by the original atlas owners.

Download

The download packages include a labeled volume file (Amira am format, which can also be loaded in ImageJ), surface representations of individual bones of the segmented skeleton and the skin in the STL format, a list with joint coordinates and a small documentation. To apply for downloading the atlas files, please fill out thisform. You will then receive an email with further instructions.

Links and references to the original atlases

  • MOBY Atlas
    • Segars, W. P.; Tsui, B. M. W.; Frey, E. C.; Johnson G. A. and Berr, S. S. Development of a 4D digital mouse phantom for molecular imaging research. Mol. Imag. Biol. 6(3):149-159, 2004.
    • For further information on the MOBY phantom, please contactpaul.segars@duke.edu.
  • Digimouse Atlas
    • Dogdas, B.; Stout, D.; Chatziioannou, A. and Leahy, R. M. Digimouse: a 3D whole body mouse atlas from CT and cryosection data”. Phys. Med. Biol.52(3):577-587, 2007.
  • SD Rat atlas
    • Wu, L.; Zhang, G.; Luo, Q. and Liu, Q. An image-based rat model for Monte Carlo organ dose calculations. Med. Phys. 35(8): 3759-3764, 2008.
    • Bai, X.; Yu, L.; Liu, Q.; Zhang, J.; Li, A.; Han, D.; et al. A high-resolution anatomical rat atlas. J. Anat. 209(5):707-708, 2006.

Contact information

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