Hippocampus Diencephalon


AMBMC » Hippocampus

Hippocampal formation: MR image segmentation guide

High-resolution MR images were acquired using a 16.4T imaging system and the hippocampal formation was segmented using DISPLAY (1). To assist segmentation of the hippocampal formation, MR images of an adult male C57BL/6 mouse brain are provided as a series of unsegmented and segmented images in the coronal plane (example below). The 25 image sets at 300m intervals commence approximately 0.80 mm caudal to bregma and ending 4.80 mm caudal to bregma. Follow the links to view series of segmented MR images. Details of the operational guidelines used for systematic segmentation of the hippocampal formation please refer to the segmentation guide.


Segmentation was based chiefly on the atlases of Franklin and Paxinos (2008), and Dong (2008). Please note, segmentation includes correction to region defined as perirhinal cortex in mouse, not shown in these atlases.

atlas (with labels)

Use the buttons as a navigational tool for regions of the hippocampal formation (HF). Move the mouse over the left hemisphere of MR images and segmented image to identify HF structures. Note: structures that appear on right hemisphere only are labelled.

For more details about the segmentation please see:

Richards K, Watson C, Buckley RF, Kurniawan ND, Yang Z, Keller MD, Beare R, Bartlett PF, Egan GF, Galloway GJ, Paxinos G, Petrou S, Reutens DC. Segmentation of the mouse hippocampal formation in magnetic resonance images. Neuroimage. 2011 Oct 1;58(3):732-40. doi: 10.1016/j.neuroimage.2011.06.025. Epub 2011 Jun 17.

Pubmed Link

Download the data in MINC or NiFTI format here:


   ambmc-c57bl6-model-nonsym_v0.8 [ mnc | nii ]

Label files (including index)

   ambmc-c57bl6-label-hippocampus_v0.8 [ mnc | nii ]

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