Many mouse brain coordinate systems exist. Which one should become the standard? Alternatively, can multiple coordinate systems coexist but become interoperable? Who will set the standards?

The new paper “Waxholm Space: An image-based reference for coordinating mouse brain research” published November 1, 2010 in NeuroImage presents a new coordinate system for the mouse brain and suggests that this should be the standard moving forward. Why should we take their suggestion seriously?

The new system is named Waxholm Space (WHS). Waxholm was the Swedish city where, in February of 2007, a group of scientists was assembled through the International Neuroinformatics Coordinating Facility (INCF) to discuss what they might do to help coordinate data from research in the mouse brain. They decided on establishing a reference atlas of the mouse brain that would act as a universal coordinate system for mouse data.

They used data from Magnetic Resonance Imaging (MRI) and conventional Nissl histology on brains from the standard C57BL/6 mouse. The data are the highest resolution acquired by any atlas to date at 21.5 cubic micrometers.

The fact that the INCF is committed to supporting and maintaining WHS provides a solid reason for using WHS as the mouse brain standard. Another reason is that all of the data used to create the space and the atlas are available to the public. Finally, there is apparently commitment by the INCF and/or the Neuroscience Information Framework (NIF) teams to support transformations amongst the various coexisting coordinate systems out there.

Note: A good place to access documentation and raw data on the Waxholm Space Atlas is at the INCF website here.


Other related blog posts:

NeuronBank: Neuronal Circuit Online Data Repository

Whole Brain Catalog: the Google Earth for the Brain

Whole Brain Catalog: Brain Cells and Molecules

Bio-Commons a Global Challenge

Whole Brain Catalog: Visualizing Neural Network Activity