A multicontrast MR atlas of the Wistar rat brain

Abstract

We describe a multi-contrast, multi-dimensional atlas of the Wistar rat acquired at microscopic spatial resolution using magnetic resonance histology (MRH). Diffusion weighted images, and associated scalar images were acquired of a single specimen with a fully sampled Fourier reconstruction, 61 angles and b=3000 s/mm 2 yielding 50 um isotropic spatial resolution. The higher angular sampling allows use of the GQI algorithm improving the angular invariance of the scalar images and yielding an orientation distribution function to assist in delineating subtle boundaries where there are crossing fibers and track density images providing insight into local fiber architecture. A multigradient echo image of the same specimen was acquired at 25 um isotropic spatial resolution. A quantitative susceptibility map enhances fiber architecture relative to the magnitude images. An accompanying multi-specimen atlas (n=6) was acquired with compressed sensing with the same diffusion protocol as used for the single specimen atlas. An average was created using diffeomorphic mapping. Scalar volumes from the diffusion data, a T2* weighted volume, a quantitative susceptibility map, and a track density volume, all registered to the same space provide multiple contrasts to assist in anatomic delineation. The new template provides significantly increased contrast in the scalar DTI images when compared to previous atlases. A compact interactive viewer based on 3D Slicer is provided to facilitate comparison among the contrasts in the multiple volumes. The single volume and average atlas with multiple 3D volumes provide an improved template for anatomic interrogation of the Wistar rat brain. The improved contrast to noise in the scalar DTI images and the addition of other volumes (eg. QA,QSM,TDI ) will facilitate automated label registration for MR histology and preclinical imaging.

Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System

“…Uncovering complex functions of the brain for understanding disease mechanisms and developing effective therapies requires a combination of multiple neuroimaging techniques. Integration of in vivo and ex vivo tissue probing modalities, such as magnetic resonance imaging (MRI) and histology, has been described previously as it would enable researchers to study both temporal changes in a living brain as well as molecular markers in the same tissue post-mortem [1][2][3][4][5][6][7][8][9][10][11][12] .…”

Development and advancements in rodent MRI-based brain atlases

“…As can be seen from the table, the rat MRI brain atlas was developed primarily based on adult male Sprague-Dawley and Wistar rats. Among them, the highest spatial resolution of MR images based on ex vivo and in vivo rat brain tissue is 0.025 × 0.025 × 0.025 (mm3) [ [64] , [65] , [66] ], and 0.088 × 0.088 × 0.088 (mm 3 ) [ 77 ], respectively. The most widely used of these rat brain atlases are the Schwarz (DPABI) and Waxholm 1.0 atlases, published by Schwarz, A. J. and Papp, E. A. in 2006 and 2014, respectively [ 29 , 30 ].…”

“…Spatial resolution and contrast of MR images are two key features commonly used to compare the quality of MRI brain atlases [ 64 ]. The use of MRI brain atlases is ultimately determined by these two significant, linked aspects.…”

“…A recent milestone includes the practical development of a 3D mouse brain atlas based on histological data [ 13 ]. Furthermore, digital atlases derived from multi-sequence data have emerged in the field of MRI brain atlases, enabling the mapping of a larger number of brain regions with higher precision [ 64 ]. The efficacy of brain atlases relies on the inclusion of high-resolution anatomical images that exhibit rich anatomical contrast and precise structural delineation.…”