Segmentation of the mouse hippocampal formation in magnetic resonance images
Research highlights
► Development of an MR-based mouse hippocampal atlas ► Delineation of the anatomical boundaries of 40 hippocampal sub-regions ► Volumetric analysis of hippocampal structures in the adult mouse brain
Introduction
The hippocampal formation is made up of a number of distinct regions. It includes the hippocampus proper (which consists of the cornu ammonis (CA) fields 1–3 and the dentate gyrus (DG)), the subiculum and adjacent presubiculum, postsubiculum, and parasubiculum, the entorhinal cortex, the perirhinal cortex, and rudimentary components of the hippocampus (indusium griseum, dorsal tenia tecta, and ventral tenia tecta) (Amaral et al., 2007, Andersen, 2007). Structural changes in the hippocampus have recently been studied using MR in mouse models of human disease, including Alzheimer's disease (Borthakur et al., 2006, Lau et al., 2008) and Huntington's disease (Sawiak et al., 2009). Until recently, the value of digital atlases of the hippocampus has been limited by inadequate resolution in MR images, resulting in difficulty distinguishing regional boundaries (Ma et al., 2005, Chen et al., 2006). The use of high resolution MR has made possible the visualization of anatomical structures at a level of detail approaching that of histological preparations (Mueller et al., 2007, Boretius et al., 2009). This has resulted in the emergence of MR imaging atlases with increasing levels of anatomical detail (Benveniste et al., 2000, MacKenzie-Graham et al., 2004, Kovacevic et al., 2005, Badea et al., 2007, Dorr et al., 2008, Johnson et al., 2010).
Harnessing the resolution available with high-field MR imaging requires reproducible methods that allow consistent segmentation of hippocampal structures across mouse brains. One of the difficulties in separating the many sub-regions within the hippocampal formation is the lack of agreed guidelines for defining the boundaries of each region. Our aim was to generate a set of operational criteria for the segmentation of over 40 structures in the hippocampal formation in MR images. These operational criteria are supplemented with a digital atlas and brief description of each region to assist others who may wish to utilize our segmentation protocol. We developed a hippocampal atlas that is consistent with the segmentation of images of histological sections.
Section snippets
C57BL/6J mouse brain preparation and magnetic resonance imaging
All procedures involving animals were approved by the University of Queensland Animal Ethics Committee (AEC: CMR/907/08/NHMRC). A twelve-week old male inbred C57BL/6J mouse was initially anesthetized with isoflurane. Prior to perfusion, the mouse was injected with 0.02 ml/g of pentobarbitone sodium (Lethabarb). Using a Perfusion One® system (MyNeuroLab, St Louis, MO, USA), the mouse circulation was flushed with 0.1 M phosphate buffer (PB; pH 7.4) and then fixed with a solution containing 4%
Results
The hippocampal formation was segmented into major regions and sub-regions as summarized in Table 1. The level of contrast in the CA and DG sub-regions and their layers enabled ready delineation (Fig. 1). On the other hand, subdivisions of the entorhinal cortex (Fig. 2) were difficult to segment because of the lack of definitive contrast. We supplemented our interpretation of the MR images with data from Nissl stained sections as well as in situ hybridization data for gene expression from
Discussion
We have developed a method for the systematic segmentation of the hippocampal formation in MR images in the mouse. In developing the operational criteria for segmentation we have supplemented MR findings with data from cytoarchitecture and gene expression studies. This is the first MR image segmentation that outlines the hippocampal structures in such detail. The method we have developed is applicable to studies that attempt to analyze changes in the hippocampus in mouse models of neurological
Conclusion
This study presents a new method for the systematic and detailed segmentation of MR images of the hippocampal formation in the mouse brain. This method provides the criteria for future development of a probabilistic atlas of the hippocampal formation, where data acquired from a large number of brains will be used to produce a canonical reference to which mutant strains can be compared.
Acknowledgments
We thank the Queensland NMR Network (QNN) and the National Imaging Facility (NIF) for instrument access and technical support. This work was funded by the National Health and Medical Research Council (NHMRC) of Australia.
References (46)
- et al.
Magnetic resonance microscopy of the C57BL mouse brain
NeuroImage
(2000) - et al.
MRI of cellular layers in mouse brain in vivo
NeuroImage
(2009) - et al.
Neuroanatomical differences between mouse strains as shown by high-resolution 3D MRI
NeuroImage
(2006) - et al.
Parkinson's disease: mechanisms and models
Neuron
(2003) - et al.
High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice
NeuroImage
(2008) - et al.
Waxholm space: an image-based reference for coordinating mouse brain research
NeuroImage
(2010) - et al.
Defining the human hippocampus in cerebral magnetic resonance images—an overview of current segmentation protocols
NeuroImage
(2009) - et al.
Longitudinal neuroanatomical changes determined by deformation-based morphometry in a mouse model of Alzheimer's disease
NeuroImage
(2008) - et al.
A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy
Neuroscience
(2005) - et al.
Measurement of hippocampal subfields and age-related changes with high resolution MRI at 4 T
Neurobiol. Aging
(2007)
Mechanisms of human inherited epilepsies
Prog. Neurobiol.
Use of magnetic resonance imaging for anatomical phenotyping of the R6/2 mouse model of Huntington's disease
Neurobiol. Dis.
The dentate gyrus: fundamental neuroanatomical organization (dentate gyrus for dummies)
Prog. Brain Res.
The Hippocampus Book
MRI of mouse models of neurological disorders
NMR Biomed.
Neuroanatomical phenotypes in the reeler mouse
NeuroImage
Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy
Methods
In vivo measurement of plaque burden in a mouse model of Alzheimer's disease
J. Magn. Reson. Imaging
Resolution enhancement in MRI
Magn. Reson. Imaging
Application of magnetic resonance imaging to study pathophysiology in brain disease models
Methods Mol. Med.
The Allen Reference Atlas: A Digital Color Brain Atlas of the C57BL/6J Male Mouse
Identification of a set of genes showing regionally enriched expression in the mouse brain
BMC Neurosci.
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