Development of MRI‐based atlases of non‐human brains

Abstract

Brain atlases are a fundamental resource for neuroscience research. In the past few decades they have undergone a transition from traditional printed histological atlases to digital atlases made up of multiple data sets from multiple modalities, and atlases based upon magnetic resonance imaging (MRI) have become widespread. In this article we discuss the methods involved in making an MRI brain atlas, including registration of multiple data sets into a model, ontological classification, segmentation of a minimum deformation model, dissemination strategies, and applications of these atlases. Finally we discuss possible future directions in the development of brain atlases.

An ontologically consistent MRI-based atlas of the mouse diencephalon

“…Images were placed in the stereotaxic coordinate space and a symmetric model was created using a recursive non-linear hierarchical fitting strategy (Janke and Ullmann, 2015;Ullmann et al, 2015). Briefly, the fitting strategy consisted of 3 linear fits to the evolving internal model followed by a hierarchical series of non-linear grid transforms.…”

“…Interpolation resulted in a model with 15 μm 3 isotropic voxels. For a detailed description of the model creation see Janke and Ullmann (2015).…”

“…CW and GP are authors of a number of highly cited rodent brain atlases (Paxinos and Franklin, 2013); Paxinos and Watson, 2014;Paxinos et al, 2009;Watson and Paxinos, 2010) and JFPU is experienced in the development of MRI-based atlases of vertebrates (Ullmann et al, 2010;Ullmann et al, 2015;Ullmann et al, 2010b). The operational criteria for defining anatomical features were defined in terms of differences in signal intensity and their location with reference to anatomical landmarks.…”

“…Additionally, a symmetric average mouse brain MRI model is included in the package that should be used for image registrations (Janke and Ullmann, 2015). Users of this package are also provided with a configuration file, which contains the suggested parameters for performing non-linear registration of a 30 μm mouse brain T 2 *-weighted MRI to the 15 μm AMBMC T 2 *-weighted mouse brain model in FSL (FNIRT).…”

Magnetic Resonance Imaging of the Brain of a Monotreme, the Short-Beaked Echidna (<b><i>Tachyglossus aculeatus</i></b>)

“…For this, a series of tif images was generated from the above T1-and T2-weighted data sets using ImageJ (version 2.0) software and these images were imported into Adobe Illustrator (version CS5.1) for delineation and region labeling. As per recommendations for mapping of MRI images [Ullmann et al, 2015], delineation was confined to one side of a coronal image so that structures on the other side remained visible and signal contrast between brain regions could be assessed by eye without distracting labels.…”