Publications (15) View all
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Article: Correction: digital atlasing and standardization in the mouse brain.
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ABSTRACT: [This corrects the article on p. e1001065 in vol. 7.].PLoS Computational Biology 02/2011; 7(2). · 5.22 Impact Factor -
Article: Digital atlasing and standardization in the mouse brain.
PLoS Computational Biology 01/2011; 7(2):e1001065. · 5.22 Impact Factor -
Article: A genome-scale map of expression for a mouse brain section obtained using voxelation.
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ABSTRACT: Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological diseases. We have reconstructed two-dimensional images of gene expression for 20,000 genes in a coronal slice of the mouse brain at the level of the striatum by using microarrays in combination with voxelation at a resolution of 1 mm3. Good reliability of the microarray results were confirmed using multiple replicates, subsequent quantitative RT-PCR voxelation, mass spectrometry voxelation, and publicly available in situ hybridization data. Known and novel genes were identified with expression patterns localized to defined substructures within the brain. In addition, genes with unexpected patterns were identified, and cluster analysis identified a set of genes with a gradient of dorsal/ventral expression not restricted to known anatomical boundaries. The genome-scale maps of gene expression obtained using voxelation will be a valuable tool for the neuroscience community.Physiological Genomics 09/2007; 30(3):313-21. · 2.73 Impact Factor -
Article: Brain atlases and neuroanatomic imaging.
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ABSTRACT: Quantifying the effect of a genetic manipulation or disease is a complicated process in a population of animals. Probabilistic brain atlases can capture population variability and be used to quantify those variations in anatomy as measured by structural imaging. Minimum deformation atlases (MDAs), a subclass of probabilistic atlases, are intensity-based averages of a collection of scans in a common space unbiased by selection of a single target image. Here, we describe a method for generating an MDA from a set of magnetic resonance microscopy images. First, the images are segmented to remove any non-brain tissue and bias field corrected to remove field inhomogeneities. The corrected images are then linearly aligned to a representative scan, the geometric mean of all the transformations is calculated, and a minimum deformation target (MDT) is produced by averaging the volumes in this new space. The brains are then non-linearly aligned to the MDT to produce the MDA. Finally, the images are linearly aligned to the MDA using a full-affine transformation to spatially and intensity normalize them, removing global differences in size, shape, and position but retaining anatomically significant differences.Methods in molecular biology (Clifton, N.J.) 02/2007; 401:183-94. -
Article: Cerebellar cortical atrophy in experimental autoimmune encephalomyelitis.
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ABSTRACT: Brain atrophy measured by MRI is an important correlate with clinical disability and disease duration in multiple sclerosis (MS). Unfortunately, neuropathologic mechanisms which lead to this grey matter atrophy remain unknown. The objective of this study was to determine whether brain atrophy occurs in the mouse model, experimental autoimmune encephalomyelitis (EAE). Postmortem high-resolution T2-weighted magnetic resonance microscopy (MRM) images from 32 mouse brains (21 EAE and 11 control) were collected. A minimum deformation atlas was constructed and a deformable atlas approach was used to quantify volumetric changes in neuroanatomical structures. A significant decrease in the mean cerebellar cortex volume in mice with late EAE (48-56 days after disease induction) as compared to normal strain, gender, and age-matched controls was observed. There was a direct correlation between cerebellar cortical atrophy and disease duration. At an early time point in disease, 15 days after disease induction, cerebellar white matter lesions were detected by both histology and MRM. These data demonstrate that myelin-specific autoimmune responses can lead to grey matter atrophy in an otherwise normal CNS. The model described herein can now be used to investigate neuropathologic mechanisms that lead to the development of gray matter atrophy in this setting.NeuroImage 10/2006; 32(3):1016-23. · 5.89 Impact Factor
