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Waxholm Space Atlas

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Waxholm Space is a coordinate-based reference space for the mapping and registration of neuroanatomical data in the mouse brain


Here you can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain. These images include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution.

The label volume represents phase one delineations of the WHS mouse brain. The atlas contains 26 structures (+ inner ear) organized in accordance with the NeuroLex Brain Partonomy scheme found at: The delineations are intended as a communication aid for finding brain locations. Delineations are based on visually distinguishable features and are not intended to impose a specific view of brain structure or function.

The Community Site for Waxholm Space ( contains information for end users and developers wishing wishing to register or share their data.




Datasets are provided as gzipped NIFTI file (no decompression necessary for many viewers, e.g., FreeSurfer, FSLView). Smaller, downsampled volumes at 43μ resolution are also available. The labelled dataset contains the WHS atlas T2* image data at full and half resolution in NIfTI format (.nii), corresponding label images in NIfTI format, text labels grouped in accordance with NeuroLex Brain Partonomy as of 19-Nov-2010 in an xml format (.ilf) and two MBAT atlas xml files (.atlas). The data is ready for use in the Mouse BIRN Atlasing Toolkit (MBAT).

Ease of Use

Anyone can use it



Operating system

Waxholm Space (MBAT)


This tool has been downloaded 17301 times.
  • 5 files
  • 1 external files
  • 2 documentation item
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