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Cited by 113Advanced Neuroimaging Techniques and ApplicationsAdvanced MRI Techniques and ApplicationsAnatomy and Medical Technology

A multidimensional magnetic resonance histology atlas of the Wistar rat brain

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Johnson, G. Allan, Calabrese, Evan, Badea, Alexandra, Paxinos, George, Watson, Charles·2012·NeuroImage
DOI 10.1016/j.neuroimage.2012.05.041PMC PMC3408821
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Abstract

We have produced a multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). This MR atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies.

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  • Applying parallel imaging and SMS techniques to studies in the mouse brain is challenging due to the small coil size and limited space in the probe.

    “Applying these techniques to studies in the mouse brain is challenging due to the small coil size (supplemental figure 1) and the limited space in the probe (Johnson et al. 2012; Petiet et al. 2008; Larkman and Nunes 2007).”

    From Neurite orientation dispersion and density imaging of mouse brain microstructure (2019) · cites this paper as Johnson et al. 2012

    Methods §2.2 describes a 30-mm solenoid RF coil used for rat-brain imaging, and the Introduction discusses mouse atlases. Neither passage addresses whether small coils or limited probe space make parallel imaging or SMS challenging in mouse-brain studies (searched: parallel imaging, SMS, coil size, probe space). (LLM, conf=0.75)

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References 48 · Cited by 113

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Authors
Johnson, G. A., Calabrese, E., Badea, A., Paxinos, G., & Watson, C.
Affiliations
  • Duke University (US)
  • UNSW Sydney (AU)
  • Curtin University (AU)
Corresponding author
Johnson, G. Allan
ORCID
Venue
NeuroImage
Publisher
Elsevier BV
Published
2012-09
Volume
62
Issue
3
Pages
1848-1856
ISSN
1053-8119 (ISSN-L)
DOI
10.1016/j.neuroimage.2012.05.041
PMC
PMC3408821
OpenAlex
W2001937826
Cited by
113
References
48
Citations by year
2026: 3 · 2025: 9 · 2024: 6 · 2023: 4 · 2022: 12 · 2021: 4 · 2020: 6 · 2019: 4 · 2018: 11 · 2017: 7 · 2016: 5 · 2015: 13 · 2014: 18 · 2013: 10 · 2012: 1
FWCI
10.14
Type
journal article
Language
en
Open access
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations
  • NeuroImage (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • eSpace (Curtin University) (submittedVersion)
Funders
National Institute of Biomedical Imaging and Bioengineering (P41EB015897)
Topics
  • Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
  • Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced MRI Techniques and Applications
  • Physical Sciences › Engineering › Biomedical Engineering › Anatomy and Medical Technology
Keywords
brain atlas, diffusion tensor imaging, white matter connectivity, neuroanatomy, isotropic resolution, data registration, brain sectioning
MeSH terms
Anatomy, Artistic, Animals, Atlases as Topic, Brain, Image Processing, Computer-Assisted, Male, Rats, Wistar, Imaging, Three-Dimensional, Diffusion Magnetic Resonance Imaging, Rats

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