Waxholm Space Atlas of the Sprague Dawley Rat Brain

Open access volumetric atlas offering comprehensive anatomical delineations of the rat brain based on structural contrast in isotropic magnetic resonance (39 μm) and diffusion tensor (78 μm) images acquired ex vivo from an 80 day old male Sprague Dawley rat at the Duke Center for In Vivo Microscopy. Spatial reference is provided by the Waxholm Space coordinate system. The location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non-structural images such as functional or pharmacological MRI and PET.

The atlas, the MRI/DTI volumes, and the diffusion tensor data are shared in NIfTI format with labels and configuration files for use with ITK-SNAP and the Mouse BIRN Atlasing Toolkit. Delineation criteria are described in Papp et al. 2014 & Kjonigsen et al. 2015 (see Docs). The latest atlas version contains 79 structures, intended as a basis for further development by researchers in the community. Missing a region? Get involved!
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Specifications

License:Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
Domain:MR, PET/SPECT
Operating System:OS Independent
Supported Data Format:NIfTI-1
Other Keywords: DTI, MRI, Template, Volumetric atlas, Waxholm Space

Associations

works well with:ITK-SNAP
MouseBIRN Atlasing Toolkit (MBAT)

Recent Activity

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File Activity

Atlas: v2.00 release

WHS_SD_v2_brainmask_bin.nii.gz posted by Eszter Agnes Papp on Feb 8

File Activity

Atlas: v2.00 release

WHS_SD_v2_white_gray_mask_clipped.label posted by Eszter Agnes Papp on Feb 8

File Activity

Atlas: v2.00 release

WHS_SD_v2_white_gray_mask_clipped.nii.gz posted by Eszter Agnes Papp on Feb 8

File Activity

Atlas: v2.00 release

WHS_SD_v2_white_gray_mask.label posted by Eszter Agnes Papp on Feb 8

File Activity

Atlas: v2.00 release

WHS_SD_v2_white_gray_mask.nii.gz posted by Eszter Agnes Papp on Feb 8

Document Activity

Main Folder documentation

Release notes v2 posted by Eszter Agnes Papp on Nov 25, 2016

Document Activity

Main Folder documentation

Release notes v1.01 posted by Eszter Agnes Papp on Nov 25, 2016

Document Activity

Main Folder documentation

Coordinates v1 - v1.01 posted by Eszter Agnes Papp on Nov 25, 2016

Document Activity

Main Folder documentation

Coordinate system orientation v1 - v1.01 posted by Eszter Agnes Papp on Nov 25, 2016

Document Activity

Publications documentation

Papp et al. 2014 posted by Eszter Agnes Papp on Nov 25, 2016