A Deformable Atlas of the Laboratory Mouse
- 813 Downloads
This paper presents a deformable mouse atlas of the laboratory mouse anatomy. This atlas is fully articulated and can be positioned into arbitrary body poses. The atlas can also adapt body weight by changing body length and fat amount.
A training set of 103 micro-CT images was used to construct the atlas. A cage-based deformation method was applied to realize the articulated pose change. The weight-related body deformation was learned from the training set using a linear regression method. A conditional Gaussian model and thin-plate spline mapping were used to deform the internal organs following the changes of pose and weight.
The atlas was deformed into different body poses and weights, and the deformation results were more realistic compared to the results achieved with other mouse atlases. The organ weights of this atlas matched well with the measurements of real mouse organ weights. This atlas can also be converted into voxelized images with labeled organs, pseudo CT images and tetrahedral mesh for phantom studies.
With the unique ability of articulated pose and weight changes, the deformable laboratory mouse atlas can become a valuable tool for preclinical image analysis.
Key wordsSmall animal imaging Mouse atlas Articulated model Atlas registration Molecular imaging
The authors thank Dr. Richard M. Leahy and Dr. Boudewijn P.F. Lelieveldt for providing the online resources of the Digimouse atlas and the articulated mouse skeleton atlas and Dr. Qianqian Fang and Dr. Bing Jian for publishing the software of iso2mesh and point set registration. We thank Dr. Anna Wu, Owen Witte, Tove Olafsen, Melissa Mccracken, Richard Tavare, Scott Knowles, Waldemar Ladno, and Darin Williams from UCLA for sharing the mouse organ weight dissection data and Dr. John David, D.V.M. for the professional comments on mouse anatomy. We also appreciate the efforts of the anonymous reviewers who helped us to improve the paper quality. This work was supported in part by SAIRP NIHNCI 2U24 CA092865 and a UCLA Chancellor’s Bioscience Core grant.
Conflict of Interest
This deformable mouse atlas contains copyrightable subject matter that has been assigned to the Regents of the University of California (UC case 2014-894).
(MP4 8.75 mb)
- 4.ITIS Foundation. ITIS Virtual Population animal models. http://www.itis.ethz.ch/itis-for-health/virtual-population/animal-models/.
- 6.Clark D, Badea A, Johnson GA, Badea CT (2013) Constructing a 4D murine cardiac micro-CT atlas for automated segmentation and phenotyping applications. Proc SPIE Med Imaging 8669:1–12Google Scholar
- 17.High resolution mouse brain atlas. http://www.hms.harvard.edu/research/brain/.
- 22.Hawrylycz M, Baldock RA, Burger A et al (2011) Digital atlasing and standardization in the mouse brain. PLoS Comput Biol 7Google Scholar
- 24.Burger A, Davidson D, Baldock R, et al. (2008) The Edinburgh mouse atlas. In: Anatomy ontologies for bioinformatics, vol. 6. Springer, London, pp. 249–265.Google Scholar
- 29.Khmelinskii A, Baiker M, Chen XJ, et al. (2010) Atlas-based organ & bone approximation for ex-vivo MRI mouse data: a pilot study. Proceedings of the 7th IEEE international symposium on biomedical imaging: from nano to macro, 1197–1200.Google Scholar
- 33.Wang H Stout DB Olafsen T and Chatziioannou AF (2011) Quantification of organ uptake from small animal PET images via registration with a statistical mouse atlas. Proceedings of the medical image computing and computer-assisted intervention (MICCAI), workshop on multi-atlas labeling and statistical fusion, 11–18.Google Scholar
- 38.ITIS Foundation. SEMCAD X numerical phantoms. http://www.speag.com/products/semcad/components/semcad-phantoms/.
- 40.Baiker M, Staring M, Löwik CWGM et al (2011) Automated registration of whole-body follow-up MicroCT data of mice. Proc Med Image Comput Comput-Assist Interv-MICCAI 6892:516–523Google Scholar
- 44.Bing J, Vemuri BC (2005) A robust algorithm for point set registration using mixture of Gaussians. Proc IEEE Int Conf Comput Vis (ICCV 2005) 2:1246–1251Google Scholar
- 45.Lewis JP, Cordner M, and Fong N (2000) Pose space deformation: a unified approach to shape interpolation and skeleton-driven deformation. Proceedings of the 27th annual conference on Computer graphics and interactive techniques, 165–172.Google Scholar
- 46.Jacka D, Reid A, Merry B, and Gain J (2007) A comparison of linear skinning techniques for character animation. Proceedings of the 5th international conference on computer graphics, virtual reality, visualisation and interaction in Africa, 177–186.Google Scholar
- 50.Wilhelms J (1995) Modeling animals with bones, muscles, and skin. Citeseer.Google Scholar
- 58.Eisen EJ (2005) The mouse in animal genetics and breeding research. Imperial College Press, London.Google Scholar
- 60.Woglom WH (1919) The size of the spleen in immune mice. J Cancer Res 4:281–323Google Scholar
- 61.Fang Q and Boas DA (2009) Tetrahedral mesh generation from volumetric binary and grayscale images. Proceedings of the biomedical imaging: from nano to macro, 2009 ISBI ’09 IEEE international symposium on, 1142–1145.Google Scholar