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

• Published in: NeuroImage (Orlando, Fla.) Vol. 78; pp. 196 - 203
• Main Authors: Ullmann, Jeremy F.P., Watson, Charles, Janke, Andrew L., Kurniawan, Nyoman D., Reutens, David C.
• Format: Journal Article
• Language: English
• Published: Amsterdam Elsevier Inc 01.09.2013; Elsevier; Elsevier Limited
• Subjects: Anatomy, Artistic; Animals; Atlases as Topic; Biological and medical sciences; Brain; Cerebral cortex; Cortex; Disorders; Downloading; Fundamental and applied biological sciences. Psychology; Gene expression; Genetics; Image Processing, Computer-Assisted; Imaging, Three-Dimensional - methods; Isocortex; Magnetic Resonance Imaging; Mice - anatomy & histology; Mice, Inbred C57BL; Neocortex - anatomy & histology; NMR; Nuclear magnetic resonance; Patterning; Segmentation; Studies; Vertebrates: nervous system and sense organs; Atlas; Magnetic resonance imaging; Segmentation; Isocortex; Cortex; Cerebral cortex; Rodentia; Central nervous system; Nuclear magnetic resonance imaging; Encephalon; Vertebrata; Mammalia; Mouse; Animal
• ISSN: 1053-8119; 1095-9572
• DOI: 10.1016/j.neuroimage.2013.04.008

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. [Display omitted] •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.