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NeuroMaps: Map Data to the Waxholm Atlas for Presentation and Publication

Filed under:

Douglas Bowden (University of Washington - Seattle), Eider Moore (University of Washington - Seattle), Shanshan Sun (University of Washington - Seattle), Mark Dubach (University of Washington - Seattle )

    NeuroMaps (2010) is a Web-based application that enables investigators to map data from mouse and macaque studies to canonical brain atlases of the two species and to edit images for presentation, publication, and archival purposes. Eventually NeuroMaps will enable investigators to view and analyze quantitatively the overlap between their data and multimodality data, such as gene expression, fMRI activation, unit activity, effects of electrical stimulation and lesion effects stored in the atlases.
    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:

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
NeuroMaps: Map Data to the Waxholm Atlas for Presentation and Publication
Two pages from the NeuroMaps website. A: The Mapper. Three cortical areas from the data image in the right panel have been mapped to the Waxholm brain in the left panel. B: The Editor. The User is editing the image size, colors, labels and dpi to download and submit for publication.
Preferred presentation format: Demo
Why demo: This abstract describes the use of a tool on the Web for mapping data to the INCF-sponsored Waxholm mouse brain atlas. The most effective way to convey how it works is to demonstrate it and allow visitors to work with it on site.
Topic: Digital atlasing

Filed under:
Andrew Davison
Andrew Davison says:
May 11, 2012 01:45 PM
I don't know enough about brain atlasing to judge the novelty of this approach, but it seems like a tool that could be useful to many congress participants.