Abstract
This paper reports the development of a high-resolution 3-D MRI atlas of the Fischer 344 adult rat brain. The atlas is a 60 μm isotropic image volume composed of 256 coronal slices with 71 manually delineated structures and substructures. The atlas was developed using Pydpiper image registration pipeline to create an average brain image of 41 four-month-old male and female Fischer 344 rats. Slices in the average brain image were then manually segmented, individually and bilaterally, on the basis of image contrast in conjunction with Paxinos and Watson’s (2007) stereotaxic rat brain atlas. Summary statistics (mean and standard deviation of regional volumes) are reported for each brain region across the sample used to generate the atlas, and a statistical comparison of a chosen subset of regional brain volumes between male and female rats is presented. On average, the coefficient of variation of regional brain volumes across all rats in our sample was 4%, with no individual brain region having a coefficient of variation greater than 13%. A full description of methods used, as well as the atlas, the template that the atlas was derived from, and a masking file, can be found on Zenodo at www.zenodo.org/record/3700210. To our knowledge, this is the first MRI atlas created using Fischer 344 rats and will thus provide an appropriate neuroanatomical model for researchers working with this strain.
Highlights
Given that the Fischer 344 rat strain is commonly used in preclinical neuroscientific research[10,11,12], and given the emergence of novel transgenic rat models generated on a Fischer 344 background[13,14,15], a digital anatomical atlas of the Fischer 344 rat brain would be of value to the scientific community
In the present study we developed a 60 μm isotropic template image of the normative Fischer 344 rat brain, from which we created an atlas comprised of 71 structures and provided a detailed basis for delineation for each structure
This paper presents a tool for preclinical researchers to identify brain structures within MR images of the Fischer 344 rat brain in a digital format, enabling rapid semi-automated structural analyses to be performed
Summary
The current study is motivated by the fact that there is currently no digital atlas for the Fischer 344 rat strain published in the literature or available online. The current atlas is the first reported atlas of the Fischer 344 rat brain. There are numerous advantages of the present atlas over currently existing rat brain atlases. The rat atlas by Schwarz et al (2006) is the only one that uses more subjects (n = 97 males) than in the current study[21]. Despite the higher number of rats used to generate their atlas, the image resolution was significantly lower than that of the atlas presented here
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