A Multidimensional Magnetic Resonance Histology Atlas of the Wistar Rat Brain

G. Allan Johnsona,b, Evan Calabresea,b, Alexandra Badeaa, George Paxinose, Charles Watsonc,d,e
     aCenter for In Vivo Microscopy, Department of Radiology, Duke University Medical Center
     bBiomedical Engineering, Box 90281 Duke University, Durham, NC 27708
     cHealth Sciences, Curtin University, Bentley, Western Australia, Australia
     dNeuroscience Research Australia, Australia
     eThe University of New South Wales, Randwick, Australia

Neuroimage 62(3): 1848-1856, 2012. PMCID: PMC3408821


Purpose: We have produced a multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). This MR atlas has been carefully aligned with the widely used Paxinos-Wats on atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies.


6 different images - all at the same coronal level demonstrate how the different acquisition and post-processing strategies highlight different anatomical regions. (a) GRE image; (b) RF refocused spin echo (b=0 mm/sec2); (c) ADC image; (d) RD image; (e) FA image; (f) color FA.


May also be of interest - Supplemental data from this link for our Rat Brain Development Atlas. Post-natal day (PND) 80 is equivalent to the adult rat atlas.

Label - Number Key:

0 - exterior 14 - accumbens nucleus
1 - cingulum 15 - fimbria/fornix
2 - midbrain 16 - corpus callosum
3 - substantia nigra 17 - amygdala
4 - anterior commissure 18 - preoptic area
5 - hindbrain 19 - isocortex
6 - septum 20 - cerebellum
7 - diagonal domain 21 - olfactory structures
8 - hypothalamus 22 - bed nucleus of stria terminalis
9 - striatum 23- pituitary
10 - diencephalon 24 - ventricles
11 - internal capsule/cerebral peduncle/pyramids 25 - optic pathways
12 - hippocampal formation 26 - pineal gland
13 - pallidum  


Supplementary Data:

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All work was performed at the Duke Center for In Vivo Microscopy, an NIH/NIBIB Biomedical Technology Resource Center (P41 EB015897). We are grateful to Sally Gewalt and James Cook for assistance with the imaging pipelines. We thank John Lee and David Lee for assistance with labeling.