A histology-based atlas of the C57BL/6J mouse brain deformably registered to in vivo MRI for localized radiation and surgical targeting.

Physics in Medicine and Biology
David PurgerEric Ford

Abstract

The C57BL/6J laboratory mouse is commonly used in neurobiological research. Digital atlases of the C57BL/6J brain have been used for visualization, genetic phenotyping and morphometry, but currently lack the ability to accurately calculate deviations between individual mice. We developed a fully three-dimensional digital atlas of the C57BL/6J brain based on the histology atlas of Paxinos and Franklin (2001 The Mouse Brain in Stereotaxic Coordinates 2nd edn (San Diego, CA: Academic)). The atlas uses triangular meshes to represent the various structures. The atlas structures can be overlaid and deformed to individual mouse MR images. For this study, we selected 18 structures from the histological atlas. Average atlases can be created for any group of mice of interest by calculating the mean three-dimensional positions of corresponding individual mesh vertices. As a validation of the atlas' accuracy, we performed deformable registration of the lateral ventricles to 13 MR brain scans of mice in three age groups: 5, 8 and 9 weeks old. Lateral ventricle structures from individual mice were compared to the corresponding average structures and the original histology structures. We found that the average structures created using our met...Continue Reading

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Citations

Oct 1, 2009·The Journal of Comparative Neurology·J L FerranL Puelles
Feb 21, 2019·Proceedings of the National Academy of Sciences of the United States of America·Ben D FulcherXiao-Jing Wang
Jun 1, 2013·Nature Methods·Pavel Osten, Troy W Margrie
Aug 6, 2013·Nature Neuroscience·Patrick KaifoshAttila Losonczy
Jul 13, 2016·European Journal of Dentistry·Natalia Díaz-GarridoRodrigo A Giacaman
Apr 17, 2018·European Journal of Dentistry·Rodrigo A GiacamanNatalia Díaz-Garrido
Jun 18, 2015·Physics in Medicine and Biology·Yidong YangJohn Wong

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