Abstract
A digital rat brain atlas, in PDF format, was derived from high-resolution in situ magnetic resonance images (MRI). The images depict transverse, sagittal, and horizontal views in contiguous 0.2 mm slices, with a planar resolution of 50 µm. Each slice was indexed to the skull surface as well as the skull landmarks Bregma and Lambda. Using a common interactive file format enables users to customize the images for their application, including image reproduction with or without background or labels. The objective was to provide an open access supplementary guide for stereotaxic neurosurgery that permits more accurate visualization of targets and determination of target coordinates in Long Evans rats. A secondary objective was to present the atlas in the widely used PDF format, not requiring specialized software for viewing, copying or unpacking. A compressed version of the atlas is available as a supplement, while an uncompressed version is available at: https://figshare.com/articles/RatAtlas_2_0_Locked_pdf/3144955.
Highlights
Numerous magnetic resonance images (MRI)-derived brain atlases are available online for multiple species (Bakker et al, 2015)
MRI-derived rat brain atlases have been produced for different purposes using different procedures
Some atlases have taken a nomothetic approach, that is to say deriving average templates from groups of animals, e.g. (Valdes-Hernandez et al, 2011) while others have taken an idiographic approach, using data derived from a single exemplar, e.g. (Papp et al, 2014)
Summary
Numerous magnetic resonance images (MRI)-derived brain atlases are available online for multiple species (Bakker et al, 2015). An early rat MRI atlas, no longer available online (Schweinhardt et al, 2003), analytically morphed their MRI images to P&W image space using an affine transformation anchored to prominent brain landmarks. From their published examples, line drawings derived from the transformed images were portrayed on a P&W coordinate grid (e.g., Figure 2), but the actual MRI images were not (e.g., Figure 3) (Schweinhardt et al, 2003). The Papp et al (2014) atlas imaged Bregma and Lambda, but did not project either the reference points or coordinates onto individual brain scans
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