NeuroMaps: Map Data to the Waxholm Atlas for Presentation and Publication
Douglas Bowden (University of Washington - Seattle), Eider Moore (University of Washington - Seattle), Shanshan Sun (University of Washington - Seattle), Mark Dubach (University of Washington - Seattle )
For the mouse the canonical brain is a symmetrical version of the MRI-based Waxholm mouse brain atlas (Johnson 2010; Bowden et al. 2011). In this demonstration we shall: 1) Show how to operate the NeuroMaps Mapper (Fig. A) and Editor (Fig. B) on the Web and 2) Explain the rationale for semiautomatic mapping to digital brain atlases in which the two sides of the brain are identical.
Major steps in the mapping and image editing procedures are:
1- Load a digital image of the brain section or surface containing the data into the right panel of NeuroMaps.
2- Load the Waxholm Atlas into the left panel.
3- Size, translate, rotate and tilt the Atlas brain (3D surface or cross section) to match the data image.
4- Click pairs of equivalent landmarks in the two images.
5- Draw the boundaries of data areas or points of data on the combined image (Fig. A).
6- Click ‘Map It’ to warp the image containing the data to the Atlas.
7- Edit colors and labels and set size and dpi parameters (Fig. B).
8- Download finished figure for publication or presentation.
NeuroMaps is freely accessible for mapping and editing figures at: http://braininfo.org
Johnson GA, Badea A, Brandenburg J, Cofer G, Fubara B, Liu S, et al. (2010) Space: an image-based reference for coordinating mouse brain research. Neuroimage;53(2):365–72.
Bowden DM, Johnson GA, Zaborsky L, Green WDK, Moore E, Badea A, Dubach MF, Bookstein (2011) A symmetrical Waxholm canonical mouse brain for NeuroMaps. Journal of Neuroscience Methods 195: 170-175.
This work was supported by the INCF and by grants from the US National Institutes of Health, MH-069259 and RR-000166 to the University of Washington