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High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology.

Publication ,  Journal Article
Johnson, GA; Ali-Sharief, A; Badea, A; Brandenburg, J; Cofer, G; Fubara, B; Gewalt, S; Hedlund, LW; Upchurch, L
Published in: Neuroimage
August 1, 2007

The Mouse Biomedical Informatics Research Network (MBIRN) has been established to integrate imaging studies of the mouse brain ranging from three-dimensional (3D) studies of the whole brain to focused regions at a sub-cellular scale. Magnetic resonance (MR) histology provides the entry point for many morphologic comparisons of the whole brain. We describe a standardized protocol that allows acquisition of 3D MR histology (43-microm resolution) images of the fixed, stained mouse brain with acquisition times <30 min. A higher resolution protocol with isotropic spatial resolution of 21.5 microm can be executed in 2 h. A third acquisition protocol provides an alternative image contrast (at 43-microm isotropic resolution), which is exploited in a statistically driven algorithm that segments 33 of the most critical structures in the brain. The entire process, from specimen perfusion, fixation and staining, image acquisition and reconstruction, post-processing, segmentation, archiving, and analysis, is integrated through a structured workflow. This yields a searchable database for archive and query of the very large (1.2 GB) images acquired with this standardized protocol. These methods have been applied to a collection of both male and female adult murine brains ranging over 4 strains and 6 neurologic knockout models. These collection and acquisition methods are now available to the neuroscience community as a standard web-deliverable service.

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Published In

Neuroimage

DOI

ISSN

1053-8119

Publication Date

August 1, 2007

Volume

37

Issue

1

Start / End Page

82 / 89

Location

United States

Related Subject Headings

  • Software
  • Sensitivity and Specificity
  • Phenotype
  • Neurology & Neurosurgery
  • Mice, Inbred C57BL
  • Mice
  • Magnetic Resonance Imaging
  • Imaging, Three-Dimensional
  • Image Processing, Computer-Assisted
  • Image Enhancement
 

Citation

APA
Chicago
ICMJE
MLA
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Johnson, G. A., Ali-Sharief, A., Badea, A., Brandenburg, J., Cofer, G., Fubara, B., … Upchurch, L. (2007). High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology. Neuroimage, 37(1), 82–89. https://doi.org/10.1016/j.neuroimage.2007.05.013
Johnson, G Allan, Anjum Ali-Sharief, Alexandra Badea, Jeffrey Brandenburg, Gary Cofer, Boma Fubara, Sally Gewalt, Laurence W. Hedlund, and Lucy Upchurch. “High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology.Neuroimage 37, no. 1 (August 1, 2007): 82–89. https://doi.org/10.1016/j.neuroimage.2007.05.013.
Johnson GA, Ali-Sharief A, Badea A, Brandenburg J, Cofer G, Fubara B, et al. High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology. Neuroimage. 2007 Aug 1;37(1):82–9.
Johnson, G. Allan, et al. “High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology.Neuroimage, vol. 37, no. 1, Aug. 2007, pp. 82–89. Pubmed, doi:10.1016/j.neuroimage.2007.05.013.
Johnson GA, Ali-Sharief A, Badea A, Brandenburg J, Cofer G, Fubara B, Gewalt S, Hedlund LW, Upchurch L. High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology. Neuroimage. 2007 Aug 1;37(1):82–89.
Journal cover image

Published In

Neuroimage

DOI

ISSN

1053-8119

Publication Date

August 1, 2007

Volume

37

Issue

1

Start / End Page

82 / 89

Location

United States

Related Subject Headings

  • Software
  • Sensitivity and Specificity
  • Phenotype
  • Neurology & Neurosurgery
  • Mice, Inbred C57BL
  • Mice
  • Magnetic Resonance Imaging
  • Imaging, Three-Dimensional
  • Image Processing, Computer-Assisted
  • Image Enhancement