An MRI-Derived Neuroanatomical Atlas of the Fischer 344 Rat Brain

Abstract

<jats:title>Abstract</jats:title><jats:p>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 at Zenodo at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://doi.org/10.5281/zenodo.3555556">https://doi.org/10.5281/zenodo.3555556</jats:ext-link>. 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.</jats:p><jats:sec><jats:title>HIGHLIGHTS</jats:title><jats:p><jats:list list-type="simple"><jats:list-item><jats:p>⍰ Open-access high-resolution anatomical MRI template for Fischer 344 rat brain.</jats:p></jats:list-item><jats:list-item><jats:p>⍰ Segmented atlas of 71 regions for use as a tool in Fischer 344 preclinical research paradigms.</jats:p></jats:list-item><jats:list-item><jats:p>⍰ Analysis of population variability of regional brain volumes.</jats:p></jats:list-item><jats:list-item><jats:p>⍰ Analysis of sex-differences in regional brain volumes</jats:p></jats:list-item><jats:list-item><jats:p>KEYWORDS: Fischer 344; Structural MRI; Segmentation; Rat brain template; Digital brain atlas; Sex-differences;</jats:p></jats:list-item></jats:list></jats:p></jats:sec>

Longitudinal characterization of neuroanatomical changes in the Fischer 344 rat brain during normal aging and between sexes

“…As such, many of our findings require additional preclinical research for confirmation, particularly the sex effects within the basal forebrain, crus 2 ansiform lobule, cingulum, commissure of the inferior colliculus, ventral pallidum, intrabulbar part of the anterior commissure, and optic chiasm, since this is the first time, to our knowledge, that these effects have been documented in the aging rodent brain. In order to properly detect the influence of sex on brain structure in future studies, it will be important to ensure the rodent brain template used is equally representative for males and females, as is the case with the Fischer rat atlas we developed in our lab and employed here (Goerzen et al 2020).…”

“…Using a Fischer 344 rat atlas generated from a 4-month cohort of wildtype Fischer 344 rats (Goerzen et al 2020) resampled into the study common space, the volumes of 73 unique regions (120 when split across hemispheres, e.g. left and right Caudoputamen) were estimated using the anatGetAll function in RMINC_1.5.2.3 (J.…”

Atlas-Based Brain Extraction Is Robust Across RAT MRI Studies

“…The workflow, presented in Figure 1, and registration configuration, which is available as a JavaScript Object Notation (JSON) file from nirodents/data, closely follows antsBrainExtraction.sh. However, the most fundamental change is the reference template; integration with TemplateFlow.org equips the workflow with programmatic access to a bank of population templates to choose from, such as Goerzen's Fischer344 template and binary brain mask [14], which artsBrainExtraction uses by default. Other adaptations to the ANTs' implementation include building the workflow with Nipype [15], and denoising the moving image using a non-local means filter [16] before it is corrected for signal inhomogeneity [13].…”