An MRI atlas of the mouse Diencephalon

In topological terms, the diencephalon lies between the hypothalamus and the midbrain. It is made up of three segments, prosomere 1 (pretectum), prosomere 2 (thalamus), and prosomere 3 (the prethalamus). A number of MRI-based atlases of different parts of the mouse brain have already been published, but none of them displays the segments the diencephalon and their component nuclei. In this study we present a new volumetric atlas identifying 89 structures in the diencephalon of the male C57BL/6J 12 week mouse. This atlas is based on an average of MR scans of 18 mouse brains imaged with a 16.4T scanner. This atlas is available for download here. Additionally, we have created an FSL package to enable nonlinear registration of novel data sets to the AMBMC model and subsequent automatic segmentation.


Download the data in MINC or NiFTI format here


ambmc-c57bl6-model-symmet_v0.8 [ mnc | nii ]

Label files (including index)

ambmc-c57bl6-label-diencephalon_v0.8 [ mnc | nii ]


If you use this data please cite

Charles Watson, Andrew L. Janke, Carlo Hamalainen, Shahrzad M. Bagheri, George Paxinos, David C. Reutens and Jeremy F.P. Ullmann, An ontologically consistent MRI-based atlas of the mouse diencephalon. - https://doi.org/10.1016/j.neuroimage.2017.05.057


You can view the labels and data online on the TissueStack online viewer