Rat - Waxholm Rat (Papp, Leergaard, Calabrese, Johnson, Bjaalie 2014)

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About this atlas

The Waxholm Rat atlas is an open access volumetric atlas of the Sprague Dawley rat brain. The is based on high resolution isotropic ex vivo T2* weighted MRI and DTI data, acquired at the Duke Center for In Vivo Microscopy at resolutions of 39 μm and 78 μm, respectively. The specimen is an 80 day old male Sprague Dawley rat.

Anatomical delineations in the atlas are based on image contrast, described in detail in the accompanying publications (Papp et al. 2014, Kjonigsen et al. 2015). The latest version of the atlas contains 79 structures, and is intended as a basis for further partitioning by researchers in the community. We have anchored the atlas to both Waxholm Space and the stereotaxic space (see Documentation).

We encourage researchers to use, distribute, and further develop this atlas, which is licensed under the Creative Commons Attribute Non-Commercial Share-Alike license.

The defining citations for this atlas template are:

1. Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) "Waxholm Space atlas of the Sprague Dawley rat brain" NeuroImage 97:374-386. [doi 10.1016/j.neuroimage.2014.04.001]
2. Kjonigsen LJ, Lillehaug S, Bjaalie JG, Witter MP, Leergaard TB (2015) "Waxholm Space atlas of the rat brain hippocampal region: Three-dimensional delineations based on magnetic resonance and diffusion tensor imaging." NeuroImage 108:441–449. [doi 10.1016/j.neuroimage.2014.12.080]
3. Sergejeva M, Papp EA, Bakker R, Gaudnek MA, Okamura-Oho Y, Boline J, Bjaalie JG, Hess A (2015) "Anatomical landmarks for registration of experimental image data to volumetric rodent brain atlasing templates." Journal of Neuroscience Methods 240:161-169. [doi 10.1016/j.jneumeth.2014.11.005]

• T2*: Anatomical MRI, T2*-weighted gradient echo image at 39 μm original resolution (512x1024x512 voxels)
  • ../../templates/PLCJB14/source/WHS_SD_rat_T2star_v1.01_downsample2.nii.gz; filesize 56848 kB; shape [256x512x256]
  • ../../templates/PLCJB14/source/WHS_SD_rat_T2star_v1.01_downsample3.nii.gz; filesize 17013 kB; shape [170x341x170]
• labels: Volumetric atlas of 76 anatomical structures. The Scalable Brain Atlas template is derived from this volume.
  The label index mapper converts label indices to acronyms, full names, and rgb-values.
  • ../../templates/PLCJB14/source/WHS_SD_rat_atlas_v1.01_downsample2.nii.gz; filesize 1276 kB; shape [256x512x256]
  • ../../templates/PLCJB14/source/WHS_SD_rat_atlas_v1.01_downsample3.nii.gz; filesize 451 kB; shape [170x341x170]
• coronal_svg: Coronal sections of the label volume "WHS_SD_rat_atlas_v1.01_121.nii", converted to Scalable Vector Graphics.
  Brain regions are color-coded by the RGB to Acronym map, which can be chained with the Acronym to Fullname map.
  • ../../templates/PLCJB14/source/coronal_svg.zip; filesize 3875 kB
• wholebrain_mesh: surface mesh of the entire brain
  • ../../templates/PLCJB14/wholebrain.x3d; filesize 4660 kB