Hippocampus Diencephalon


AMBMC » Diencephalon

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 at Additionally, we have created an FSL package to enable nonlinear registration of novel data sets to the AMBMC model and subsequent automatic segmentation.


Eighteen animals were perfused and fixed with 4% paraformaldehyde and 0.1% Magnevist®. Brains were extracted and incubated in 0.1% Magnevist/PB for 4 days, placed in Fomblin and imaged on a 16.4T (89mm) Bruker micro-imaging system using a 15 mm SAW coil (M2M Imaging, USA). MRI data were acquired using a 3D gradient echo sequence with TR/TE/FA= 50ms/12ms/30°, 82 KHz spectral bandwidth, and 8 excitations with an acquisition time of 5h 15mins to produce T1/T2*-weighted images at 30µm3 isotropic resolution. A complete protocol can be downloaded here.

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. -

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 ]

You can view the labels and data online in TissueStack

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