In Vivo 3D Digital Atlas Database of the Adult C57BL/6J Mouse Brain by Magnetic Resonance Microscopy

Abstract

In this study, a 3D digital atlas of the live mouse brain based on magnetic resonance microscopy (MRM) is presented. C57BL/6J adult mouse brains were imaged in vivo on a 9.4 Tesla MR instrument at an isotropic spatial resolution of 100 mum. With sufficient signal-to-noise (SNR) and contrast-to-noise ratio (CNR), 20 brain regions were identified. Several atlases were constructed including 12 individual brain atlases, an average atlas, a probabilistic atlas and average geometrical deformation maps. We also investigated the feasibility of using lower spatial resolution images to improve time efficiency for future morphological phenotyping. All of the new in vivo data were compared to previous published in vitro C57BL/6J mouse brain atlases and the morphological differences were characterized. Our analyses revealed significant volumetric as well as unexpected geometrical differences between the in vivo and in vitro brain groups which in some instances were predictable (e.g. collapsed and smaller ventricles in vitro) but not in other instances. Based on these findings we conclude that although in vitro datasets, compared to in vivo images, offer higher spatial resolutions, superior SNR and CNR, leading to improved image segmentation, in vivo atlases are likely to be an overall better geometric match for in vivo studies, which are necessary for longitudinal examinations of the same animals and for functional brain activation studies. Thus the new in vivo mouse brain atlas dataset presented here is a valuable complement to the current mouse brain atlas collection and will be accessible to the neuroscience community on our public domain mouse brain atlas website.

Keywords: image registration; in vivo mouse brain atlas; magnetic resonance microscopy; mouse brain morphometry.

Figure 1

(A) Major parts of the positioning system. (B) Positioning system in place. (C) Mouse positioned supine in the stereotaxic cradle system which fits into the positioning tube that secures the RF volume coil in place.

Figure 2

The time course of the respiratory rate of seven individual C57BL/6J mice during in vivo MRI scans (over 4 hours). The rectangle on the left represents the time period which was used for animal positioning, RF coil tuning and acquisitions of anatomical scout images to assure the correct positioning of the mouse brain in the center of the magnet.

Figure 3

Left column: 100 μm isotropic-resolution scan; Right column: 100 × 100 × 200 μm³ resolution scan.

Figure 4

The percentage difference in structural volume and surface area measured from two different resolutions. The percentage difference was calculated as the measurement from the lower resolution scans (100 × 100 × 200 μm³, n = 12) subtracted that from the higher resolution scans (100 × 100 × 100 μm³, n = 12) and then divided by the former measurement. None of the structural differences were statistically significant (unpaired t-test). The abbreviations used are: Inf. colliculi = Inferior colliculi; B. forebrain-sep = Basal forebrain and septum; Int. capsule = internal capsule; R. midbrain = the rest of midbrain; R. brainstem = the rest of brainstem (i.e. pons and medulla); Sup. Colliculi = Superior colliculi; CC/Ext capsule = corpus callosum/external capsule; Ant. Commissure = Anterior commissure.

Figure 5

(A) The coronal, axial and sagittal slices of a 3D in vivo MRI mouse brain image with its structural segmentation superimposed as colored lines. (B) 3D surface reconstructed atlas with one cross section. (C) The brain interior with neocortex, olfactory bulb and brain stem hided from the view. (D) Further 3D details with the exterior capsule and the anterior commissure hidden from the view.

Figure 6

(A) The side-by-side difference of an in vivo (left half of the image) and an in vitro brain (right half of the image). (B) The in vivo atlas superimposed on (A). The ventricles are barely visible in the in vivo image (left half of the image) (as pointed out by the arrow and outlined by the in vivo atlas).

Figure 7

One axial image of the 3D MRM average in vivo brain with its atlas superimposed. The signal-to-noise ratio (SNR) is clearly superior to the single brain atlases (compare with Figures 5 and 6).

Figure 8

The average local deformation maps of: (A) 10 in vitro individual mouse brains mapped to the average in vitro brain. (B) 12 in vivo individual mouse brains mapped to the average in vivo brain. (C) 10 in vitro individual mouse brains mapped to the average in vivo brain. (D), (E) and (F): The ventral views of (A), (B) and (C), respectively. (G) A cross sectional view of (B) and (E). Note: the images are not strictly proportional. The color represents the average distance a given voxel underwent following registration of each of the individual brains to the average brain template.

Figure 9

3D views of the p-values resulted from the voxel-wise unpaired t-test between the deformation maps of the in vivo group (n = 12, Figure 8B) versus the in vitro group (n = 10, Figure 8C). (A) Dorsal view. (B) Ventral view.

Figure 10

(A) The 3D in vivo probabilistic atlas with three cross sections at different locations. The colors in the cross section show at each voxel the maximum probability of the common structure occupied by the normal C57BL/6J mouse brains (n = 12) after rigid-body alignment. The bright red color corresponds to high probability; blue color corresponds to low probability. (B) One cross section of the in vivo probabilistic atlas is displayed together with the average brain surface (The colors on the brain surface represent different structures).