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An ontology-based segmentation scheme for tracking postnatal changes in the developing rodent brain with MRI

Evan Calabresea,b,, G. Allan Johnsona,b, Charles Watsonc,d,e
     aCenter for In Vivo Microscopy, Department of Radiology, Duke University Medical Center, Durham, NC
     bBiomedical Engineering, Duke University, Durham, NC
     cHealth Sciences, Curtin University, Bentley, Western Australia , Australia
     dNeuroscience Research Australia, Australia
     eThe University of New South Wales, Randwick, Australia

Neuroimage, 67:375-384, 2013 Feb 11. PMCID: PMC3551262 Detailed guide to MRH-based segmentation of all 26 structures available from Neuroscience Lexicon wiki

The postnatal period of neurodevelopment has been implicated in a number of brain disorders including autism and schizophrenia. Rodent models have proven to be invaluable in advancing our understanding of the human brain, and will almost certainly play a pivotal role in future studies on postnatal neurodevelopment. The growing field of magnetic resonance microscopy has the potential to revolutionize our understanding of neurodevelopment, if it can be successfully and appropriately assimilated into the vast body of existing neuroscience research. In this study, we demonstrate the utility of a developmental neuro-ontology designed specifically for tracking regional changes in MR biomarkers throughout postnatal neurodevelopment. Using this ontological classification as a segmentation guide, we track regional changes in brain volume in rats between postnatal day zero and postnatal day 80 and demonstrate differential growth rates in axial versus paraxial brain regions. Both the ontology and the associated label volumes are provided as a foundation for future MR-based studies of postnatal neurodevelopment in normal and disease states.

Supplementary Figure 1: The six coronal levels used for assessing alignment of MRH data to the Paxinos and Ashwell histology atlas. Plates from the histology atlas (left) are shown adjacent to the corresponding MRH slice (right) after manual alignment. A-F are presented in rostral to caudal order. Note that B is the same level shown in Figure 1 of the manuscript.

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Label Key:

Link to downloadable Label Key text file

Link to tiff image of Label Key

p0 Data:

p80 Data:


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All work was performed at the Duke Center for In Vivo Microscopy, an NIH/NIBIB Biomedical Technology Resource Center (P41 EB015897). We are grateful to Sally Gewalt and James Cook for assistance with the imaging pipelines. We thank Dr. Yi Qi and Gary Cofer for assistance in specimen preparation and scanning. We thank John Lee and David Joseph Lee for assistance with labeling, and Sally Zimney for assistance in editing.