High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice

Distinct cerebellar foliation anomalies in a CHD7 haploinsufficient mouse model of CHARGE syndrome

“…Regional volumes were determined using a pre‐existing classified MRI atlas encompassing 159 different structures throughout the brain (Dorr, Lerch, Spring, Kabani, & Henkelman, 2008; Steadman et al, 2014; Ullmann, Watson, Janke, Kurniawan, & Reutens, 2013). Statistical analyses were applied comparing the absolute and relative volume of these 159 different regions and on a voxel‐wise basis in the brains of control and Chd7 gt/+ mice.…”

An ontologically consistent MRI-based atlas of the mouse diencephalon

“…However, segmentation of T 2 *-weighted MR images of the diencephalon is challenging; in comparison to the hippocampus, which has clear boundaries between layers, and the cerebellum, which has clear structural boundaries, many parts of the diencephalon possess relatively subtle variations in contrast. In many previous MR studies in the components of the thalamus were not identified (Dorr et al, 2008), with the study by Moldrich et al (2010) being the only one to attempt to segment the thalamus.…”

“…Recently, there has been an increase in the number of studies investigating the mouse thalamus using functional, structural, and diffusion-weighted imaging (DWI) techniques to examine neurological disorders and map brain connectivity (Ferris et al, 2014;Keifer et al, 2015;Maheswaran et al, 2009;Malkova et al, 2014;Nessler et al, 2007;Richards et al, 2014;Shu et al, 2013). However, these studies have relied upon manual segmentation of the diencephalon or have used atlases that identify only a limited number of diencephalic structures (Dorr et al, 2008;Kovacevic et al, 2005;Ma et al, 2005;MacKenzieGraham et al, 2004;Ullmann et al, 2012;Ullmann et al, 2014;Ullmann et al, 2013). In response to this limitation, we have endeavoured to create a comprehensive probabilistic atlas of the C57BL/6J mouse diencephalon.…”

Assembling models of embryo development: Image analysis and the construction of digital atlases

“…Examples of such methods can be found in Ma et al (2005), Kovacevic et al (2005), Dorr et al (2008), Johnson et al (2010), andUllmann etal. (2010).…”

“…Ma et al (2005) constructed a "minimal deformation average template" as an idealized specimen minimizing the deformation required to fit any specimen of the cohort. Although average templates usually imply a better signalto-noise ratio than individual specimens and exhibit a better definition in very similar regions between specimens, they fail to faithfully model fine features and regions with a high variability, lowering their definition (Kovacevic et al, 2005;Dorr et al, 2008). Finally, some approaches used a probabilistic template (Johnson et al, 2010) where specimens' variability is represented by statistical confidence limits.…”