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Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy.
Magnetic resonance microscopy (MRM) has created new approaches for high-throughput morphological phenotyping of mouse models of diseases. Transgenic and knockout mice serve as a test bed for validating hypotheses that link genotype to the phenotype of diseases, as well as developing and tracking treatments. We describe here a Markov random fields based segmentation of the actively stained mouse brain, as a prerequisite for morphological phenotyping. Active staining achieves higher signal to noise ratio (SNR) thereby enabling higher resolution imaging per unit time than obtained in previous formalin-fixed mouse brain studies. The segmentation algorithm was trained on isotropic 43-mum T1- and T2-weighted MRM images. The mouse brain was segmented into 33 structures, including the hippocampus, amygdala, hypothalamus, thalamus, as well as fiber tracts and ventricles. Probabilistic information used in the segmentation consisted of (a) intensity distributions in the T1- and T2-weighted data, (b) location, and (c) contextual priors for incorporating spatial information. Validation using standard morphometric indices showed excellent consistency between automatically and manually segmented data. The algorithm has been tested on the widely used C57BL/6J strain, as well as on a selection of six recombinant inbred BXD strains, chosen especially for their largely variant hippocampus.
Duke Scholars
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Related Subject Headings
- Subtraction Technique
- Staining and Labeling
- Sensitivity and Specificity
- Reproducibility of Results
- Pattern Recognition, Automated
- Neurology & Neurosurgery
- Microscopy
- Mice, Inbred C57BL
- Mice
- Male
Citation
![Journal cover image](https://secure.syndetics.com/index.aspx?isbn=/lc.gif&issn=1053-8119&client=dukeuniv)
Published In
DOI
ISSN
Publication Date
Volume
Issue
Start / End Page
Location
Related Subject Headings
- Subtraction Technique
- Staining and Labeling
- Sensitivity and Specificity
- Reproducibility of Results
- Pattern Recognition, Automated
- Neurology & Neurosurgery
- Microscopy
- Mice, Inbred C57BL
- Mice
- Male