Waxholm Space

The Waxholm Space (WHS) is a coordinate-based reference space that is intended to encourage interoperability between existing and future mouse data resources.

  • Developed from high resolution MR and Nissl stain image stacks
  • Allows mapping and registration of neuroanatomical data in the mouse brain
  • Provides translations among other mouse brain atlases

The Waxholm Space (WHS) atlas acts as the hub of an infrastructure connecting data and key reference spaces. Reference atlases that have been mapped to this space are “standardized” and can be used to share their associated data and services in a manner that is meaningful to external users. 

Clockwise from upper left, resources may include neuroanatomic reference atlases, large-scale gene expression databases, developmental databases, MRI and DTI imaging, histological data, analysis tools, online applications, and other 3-D anatomic models.

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Download WHS

Download the canonical WHS dataset and best practice documents from 

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E. Papp, et al. Waxholm Space atlas of the Sprague Dawley rat brain Neuroimage 2014 Apr 11. pii: S1053-8119(14)00241-9.

M. Hawrylycz, et al. Digital Atlasing and Standardization in the Mouse Brain. PLoS Comput Biol 2011;7(2):e1001065.

G.A. Johnson, et al.Waxholm Space: An image-based reference for coordinating mouse brain research. Neuroimage  2010;53(2):365-72.

Contact details

Are you a scientist with expertise in this area, and want to be involved?

Contact INCF Program Officer:

Mathew Abrams
INCF Secretariat