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An atlas of the rat brain to better understand the human brain

A team from NeuroSpin, in collaboration with researchers from the Sainte-Anne Hospital and from the University of Minho, has developed, using magnetic resonance imaging, a unique set of resources for the analysis and visualization of preclinical data in the rat brain. This work, published in Nature Communications, demonstrates the interest for such resources, both in fundamental and translational research in neuroscience.

Published on 27 January 2020

Magnetic Resonance Imaging (MRI) is a powerful diagnostic and research tool, particularly in the field of neuroscience. Typically, in this area of research, brain images acquired for several individuals of a study cohort must be made comparable with each other. In other words, factors such as individual variations in the size and shape of the brain need to be corrected and homogenized across the studied population. To achieve this goal, researchers refer to template images that represent, like geographic atlases, the brain space divided into regions of interest, either anatomical or functional (mapping the brain activity). While several reference images already exist for the analysis of human brain data, such as the Montréal Neurological Institute template, very few similar resources exist for the rodent brain. However, they remain a necessity in key contexts of research. For example, the identification of structural and/or functional changes in the rodent brain associated with the normal and pathological responses to stress is fundamental to better understanding phenomena such as vulnerability to stress, which can induce in humans a disruption of emotional regulatory processes, a decrease of cognitive performance and an accelerated emergence of psychiatric diseases such as depression.

A team from NeuroSpin, in collaboration with the Centre for Psychiatry and Neurosciences from the Sainte-Anne Hospital (Paris) and with the Medicine School of the University of Minho (Braga, Portugal), worked on creating an anatomical template and a set of atlases for the rat brain. Using a MRI acquisition protocol optimized at very high magnetic field, the researchers first obtained a series of ex vivo anatomical images exhibiting a very high isotropic spatial resolution 
(90 mm in the three dimensions), from which they created an anatomical template of the rat brain. They also generated a matching anatomical atlas composed of 246 labeled regions of interest. Finally, the analysis of functional MRI data acquired at rest led to the creation of a functional atlas of the rat brain composed of 59 regions of interest.

All these templates and atlases, gathered under the name of "The SIGMA Brain Resources", provide a unique reference space for the analysis and visualization of imaging data, as well as any other biological parameter that can be "projected" into the anatomical template. These resources, available through the NTIRC platform (, were created not only with the aim of promoting a standardized multi-centric fundamental research, but also to accelerate the translational research in neuroscience, by facilitating the use of methodologies already developed for the analysis of the human brain. The SIGMA resources have already been used to explore the structural and functional modifications of the brain induced by different chronic pathologies, as well as to characterize the pharmacological effects of certain drugs on brain activity (see references below).

Contact: Sébastien Mériaux

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