An ontologically consistent MRI-based atlas of the mouse diencephalon
Charles Watson,
Andrew L. Janke,
Carlo Hamalainen,
Shahrzad M. Bagheri,
George Paxinos,
David C. Reutens,
Jeremy F.P. Ullmann
Affiliations
Charles Watson
The Australian Mouse Brain Mapping Consortium, The University of Queensland, Brisbane, Australia; Health Sciences, Curtin University, Perth, Western Australia, Australia; Neuroscience Research Australia and The University of New South Wales, Sydney, Australia; Correspondence to: 14 Little High St, Fremantle, WA 6160, Australia.
Andrew L. Janke
The Australian Mouse Brain Mapping Consortium, The University of Queensland, Brisbane, Australia; Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
Carlo Hamalainen
Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
Shahrzad M. Bagheri
Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
George Paxinos
Neuroscience Research Australia and The University of New South Wales, Sydney, Australia
David C. Reutens
The Australian Mouse Brain Mapping Consortium, The University of Queensland, Brisbane, Australia; Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
Jeremy F.P. Ullmann
The Australian Mouse Brain Mapping Consortium, The University of Queensland, Brisbane, Australia; Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia; Department of Neurology, Boston Children's Hospital, Boston, MA, USA
In topological terms, the diencephalon lies between the hypothalamus and the midbrain. It is made up of three segments, prosomere 1 (pretectum), prosomere 2 (thalamus), and prosomere 3 (the prethalamus). A number of MRI-based atlases of different parts of the mouse brain have already been published, but none of them displays the segments the diencephalon and their component nuclei. In this study we present a new volumetric atlas identifying 89 structures in the diencephalon of the male C57BL/6J 12 week mouse. This atlas is based on an average of MR scans of 18 mouse brains imaged with a 16.4T scanner. This atlas is available for download at www.imaging.org.au/AMBMC. Additionally, we have created an FSL package to enable nonlinear registration of novel data sets to the AMBMC model and subsequent automatic segmentation.
