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Waxholm space: an image-based reference for coordinating mouse brain research.

Publication ,  Journal Article
Johnson, GA; Badea, A; Brandenburg, J; Cofer, G; Fubara, B; Liu, S; Nissanov, J
Published in: Neuroimage
November 1, 2010

We describe an atlas of the C57BL/6 mouse brain based on MRI and conventional Nissl histology. Magnetic resonance microscopy was performed on a total of 14 specimens that were actively stained to enhance tissue contrast. Images were acquired with three different MR protocols yielding contrast dependent on spin lattice relaxation (T1), spin spin relaxation (T2), and magnetic susceptibility (T2*). Spatial resolution was 21.5 mum (isotropic). Conventional histology (Nissl) was performed on a limited set of these same specimens and the Nissl images were registered (3D-to-3D) to the MR data. Probabilistic atlases for 37 structures are provided, along with average atlases. The availability of three different MR protocols, the Nissl data, and the labels provides a rich set of options for registration of other atlases to the same coordinate system, thus facilitating data-sharing. All the data is available for download via the web.

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Published In

Neuroimage

DOI

EISSN

1095-9572

Publication Date

November 1, 2010

Volume

53

Issue

2

Start / End Page

365 / 372

Location

United States

Related Subject Headings

  • Thalamus
  • Staining and Labeling
  • Reference Standards
  • Neurology & Neurosurgery
  • Mice, Inbred C57BL
  • Mice
  • Male
  • Magnetic Resonance Imaging
  • Imaging, Three-Dimensional
  • Image Processing, Computer-Assisted
 

Citation

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Johnson, G. A., Badea, A., Brandenburg, J., Cofer, G., Fubara, B., Liu, S., & Nissanov, J. (2010). Waxholm space: an image-based reference for coordinating mouse brain research. Neuroimage, 53(2), 365–372. https://doi.org/10.1016/j.neuroimage.2010.06.067
Johnson, G Allan, Alexandra Badea, Jeffrey Brandenburg, Gary Cofer, Boma Fubara, Song Liu, and Jonathan Nissanov. “Waxholm space: an image-based reference for coordinating mouse brain research.Neuroimage 53, no. 2 (November 1, 2010): 365–72. https://doi.org/10.1016/j.neuroimage.2010.06.067.
Johnson GA, Badea A, Brandenburg J, Cofer G, Fubara B, Liu S, et al. Waxholm space: an image-based reference for coordinating mouse brain research. Neuroimage. 2010 Nov 1;53(2):365–72.
Johnson, G. Allan, et al. “Waxholm space: an image-based reference for coordinating mouse brain research.Neuroimage, vol. 53, no. 2, Nov. 2010, pp. 365–72. Pubmed, doi:10.1016/j.neuroimage.2010.06.067.
Johnson GA, Badea A, Brandenburg J, Cofer G, Fubara B, Liu S, Nissanov J. Waxholm space: an image-based reference for coordinating mouse brain research. Neuroimage. 2010 Nov 1;53(2):365–372.
Journal cover image

Published In

Neuroimage

DOI

EISSN

1095-9572

Publication Date

November 1, 2010

Volume

53

Issue

2

Start / End Page

365 / 372

Location

United States

Related Subject Headings

  • Thalamus
  • Staining and Labeling
  • Reference Standards
  • Neurology & Neurosurgery
  • Mice, Inbred C57BL
  • Mice
  • Male
  • Magnetic Resonance Imaging
  • Imaging, Three-Dimensional
  • Image Processing, Computer-Assisted