Articulated Atlases Download

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 [5, 6, 8, 9, 11, 13, 17, 19, 20], for whole-body segmentation of whole-body microSPECT mouse data [3, 10, 16], whole-body MRI mouse data [1, 2, 4, 9, 14], multi-modality image combination [1, 2, 3, 4, 9, 10, 11, 15, 18] and follow-up studies [5, 8, 13 ] and proved to be a valuable tool for pre-clinical research.

atlases

For further information and details about articulated atlases construction and applications please refer to the following articles, sorted by date of publication:

  1. O. Dzyubachyk, A. Khmelinskii, E. Plenge, P. Kok, T. J. A. Snoeks, D. H. J. Poot, C. W. G. M. Löwik, C. P. Botha, W. J. Niessen, L. van der Weerd, E. Meijering and B. P. F. Lelieveldt, Interactive local super-resolution reconstruction of MRI whole-body mouse data: a pilot study with applications to bone and kidney metastases, PLoS ONE, 9(9), 2014 http://dx.doi.org/10.1371/journal.pone.0108730
  2. A. Khmelinskii , Multi-modal small-animal imaging: image processing challenges and applications,  Doctoral Thesis, Leiden University, 2013 http://hdl.handle.net/1887/21914
  3. A. Khmelinskii, H. C. Groen, M. Baiker, M. de Jong and B. P. F. Lelieveldt, Segmentation and visual analysis of whole-body mouse skeleton microSPECT, PLoS ONE, 7(11), 2012 http://dx.doi.org/10.1371/journal.pone.0048976
  4. A. Khmelinskii, E. Plenge, P. Kok, O. Dzyubachyk, D. H. J. Poot, E. Suidgeest, C. P. Botha, W. J. Niessen, L. van der Weerd, E. Meijering and B. P. F. Lelieveldt, Super-resolution reconstruction of whole-body MRI mouse data: an interactive approach, Proceedings of theIEEE International Symposium on Biomedical Imaging: From Nano to Macro, 17231726, 2012 http://dx.doi.org/10.1109/ISBI.2012.6235912
  5. M. Baiker, T.J.A. Snoeks, E.L. Kaijzel, I. Que, J. Dijkstra, B.P.F. Lelieveldt, C.W.G.M. Löwik, Automated Bone Volume and Thickness Measurements in Small Animal Whole-Body MicroCT Data, Molecular Imaging and Biology 14(4): 420–430, 2012, 10.1007/s11307-011-0522-2 http://dx.doi.org/10.1007/s11307-011-0522-2
  6. M. Baiker, Automated analysis and visualization of preclinical whole-body microCT data, Doctoral Thesis, Leiden University, 2011, http://hdl.handle.net/1887/18101
  7. T. J. Snoeks, A. Khmelinskii, B. P. F. Lelieveldt, E. L. Kaijzel and C. W. G. M. Löwik, Optical advances in skeletal imaging applied to bone metastases, Bone, 48(1): 106–114, 2011 http://dx.doi.org/10.1016/j.bone.2010.07.027
  8. M. Baiker, M. Staring, C.W.G.M. Löwik, J.H.C. Reiber, B.P.F. Lelieveldt, Automated Registration of Whole-Body Follow-Up MicroCT Data of Mice, Medical Image Computing and Computer-Assisted Intervention Lecture Notes in Computer Science 6892: 516–523, 2011http://dx.doi.org/10.1007/978-3-642-23629-7_63
  9. A. Khmelinskii, 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,Molecular Imaging and Biology, 13(5): 898–910, 2011 http://dx.doi.org/10.1007/s11307-010-0386-x
  10. A. Khmelinskii, M. Baiker, P. Kok, J. de Swart, J. H. C. Reiber, M. de Jong and B. P. F. Lelieveldt, Atlas-based articulated skeleton segmentation of μSPECT mouse data, Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 437–440, 2011 http://dx.doi.org/10.1109/ISBI.2011.5872440
  11. B.P.F. Lelieveldt, C.P. Botha, E. Kaijzel, E.A. Hendriks, Towards integrated analysis of longitudinal whole-body small animal imaging studies, Proceedings of the IEEE International Conference on Acoustics, Speech and Signal Processing, 5768 5771, 2011 http://dx.doi.org/10.1109/ICASSP.2011.5947671
  12. P. Kok, M. Baiker, E.A. Hendriks, F.H. Post, J. Dijkstra, C.W.G.M. Löwik, B.P.F. Lelieveldt, C.P. Botha, Articulated Planar Reformation for Change Visualization in Small Animal Imaging, IEEE Transactions on Visualization and Computer Graphics, 16(6): 1396–1404, 2010 http://dx.doi.org/10.1109/TVCG.2010.134
  13. 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, Medical Image Analysis, Volume 14, Issue 6, Pages: 723–737, 2010http://dx.doi.org/10.1016/j.media.2010.04.008
  14. 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-vivoμMRI mouse data: a pilot study,Proceedings of theIEEE International Symposium on Biomedical Imaging: From Nano to Macro, 1197–1200 2010, http://dx.doi.org/10.1109/ISBI.2010.5490209
  15. M. H. Wildeman, M. Baiker, J.H.C. Reiber, C.W.G.M. Löwik, 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, Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 987990, 2009 http://dx.doi.org/10.1109/ISBI.2009.5193220
  16. M. Baiker, B. Vastenhouw, W. Branderhorst, J.H.C. Reiber, F. Beekman, B.P.F. Lelieveldt, Atlas-driven scan planning for hig-resolution micro-SPECT data acquisition based on multi-view photographs: a pilot study, Proceedings of SPIE Medical Imaging: Visualization, Image-Guided Procedures, and Modeling, 7261, 2009 http://dx.doi.org/10.1117/12.813516
  17. M. Baiker, J. Dijkstra, I. Que, C.W.G.M. Löwik, J.H.C. Reiber and B.P.F. Lelieveldt Organ approximation in μCT data with low soft tissue contrast using an articulated whole-body atlas, Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 1267–1270, 2008 http://dx.doi.org/10.1109/ISBI.2008.4541234
  18. P. Kok, J. Dijkstra, C.P. Botha, F.H. Post, E. Kaijzel, I. Que, C.W.G.M. Löwik, J.H.C. Reiber, B.P.F. Lelieveldt, Integrated visualization of multi-angle bioluminescence imaging and micro CT, Proceedings of SPIE Medical Imaging: Visualization and Image-Guided Procedures, 6509, 2007 http://dx.doi.org/10.1117/12.711117
  19. M. Baiker, J. Milles, A.M. Vossepoel, I. Que, E.L. Kaijzel, C.W.G.M. Löwik, J.H.C. Reiber, J. Dijkstra and B.P.F. Lelieveldt, Fully automated whole-body registration in mice using an articulated skeleton atlas, Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 728–731, 2007 http://dx.doi.org/10.1109/ISBI.2007.356955
  20. M. Baiker, J. Dijkstra, J. Milles, C. W. G. M. Löwik and B. P. F. Lelieveldt, N. Paragios; J. Duncan & N. Ayache (ed.). Handbook of Biomedical Imaging, "Atlas-based whole-body registration in mice". Springer, N.Y., USA, in press

Acknowledgement and citation

The presented modifications to the original atlases (the manually partitioned skeletons) are free for download for academic/research purposes only.

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 the references [9] and/or [13] from the list above, along with the citation requested by the original atlas owners. To obtain the articles listed above, please send a request to one of the contacts available below.

The atlases are for personal use only, and may not be redistributed. In no event shall the LUMC be liable for any direct or indirect damage, arising in any way out of the use of these atlases.

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 this form. 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 contact paul.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

B. P. F. Lelieveldt - b.p.f.lelieveldt@lumc.nl