A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex

Ullmann, Jeremy F. P., Watson, Charles, Janke, Andrew L., Kurniawan, Nyoman D. and Reutens, David C. (2013) A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex. NeuroImage, 78 196-203. doi:10.1016/j.neuroimage.2013.04.008

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Author Ullmann, Jeremy F. P.
Watson, Charles
Janke, Andrew L.
Kurniawan, Nyoman D.
Reutens, David C.
Title A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex
Journal name NeuroImage   Check publisher's open access policy
ISSN 1053-8119
1095-9572
Publication date 2013-09-01
Year available 2013
Sub-type Article (original research)
DOI 10.1016/j.neuroimage.2013.04.008
Open Access Status File (Author Post-print)
Volume 78
Start page 196
End page 203
Total pages 8
Place of publication Netherlands
Publisher Elsevier
Language eng
Subject 2808 Neurology
2805 Cognitive Neuroscience
Abstract The neocortex is the largest component of the mammalian cerebral cortex. It integrates sensory inputs with experiences and memory to produce sophisticated responses to an organism's internal and external environment. While areal patterning of the mouse neocortex has been mapped using histological techniques, the neocortex has not been comprehensively segmented in magnetic resonance images. This study presents a method for systematic segmentation of the C57BL/6J mouse neocortex. We created a minimum deformation atlas, which was hierarchically segmented into 74 neocortical and cortical-related regions, making it the most detailed atlas of the mouse neocortex currently available. In addition, we provide mean volumes and relative intensities for each structure as well as a nomenclature comparison between the two most cited histological atlases of the mouse brain. This MR atlas is available for download, and it should enable researchers to perform automated segmentation in genetic models of cortical disorders. (C) 2013 Elsevier Inc. All rights reserved.
Formatted abstract
Highlights
• We present a methodology for delineation of the C57BL/6J mouse neocortex in MRI.
• We successfully delineated 74 neocortical and cortical-related regions.
• We calculated mean volumes and contrast intensities for each structure.

The neocortex is the largest component of the mammalian cerebral cortex. It integrates sensory inputs with experiences and memory to produce sophisticated responses to an organism's internal and external environment. While areal patterning of the mouse neocortex has been mapped using histological techniques, the neocortex has not been comprehensively segmented in magnetic resonance images. This study presents a method for systematic segmentation of the C57BL/6J mouse neocortex. We created a minimum deformation atlas, which was hierarchically segmented into 74 neocortical and cortical-related regions, making it the most detailed atlas of the mouse neocortex currently available. In addition, we provide mean volumes and relative intensities for each structure as well as a nomenclature comparison between the two most cited histological atlases of the mouse brain. This MR atlas is available for download, and it should enable researchers to perform automated segmentation in genetic models of cortical disorders.
Keyword Atlas
Cortex
Isocortex
Magnetic resonance imaging
Segmentation
Gene-expression
Automated segmentation
Alzheimers-disease
In-vivo
Brain
Microscopy
Mice
Cortex
Model
Morphometry
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID 436673
dc0
Institutional Status UQ

 
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