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. 2011 Feb 15;195(2):170-5.
doi: 10.1016/j.jneumeth.2010.11.028. Epub 2010 Dec 14.

A Symmetrical Waxholm Canonical Mouse Brain for NeuroMaps

Free PMC article

A Symmetrical Waxholm Canonical Mouse Brain for NeuroMaps

Douglas M Bowden et al. J Neurosci Methods. .
Free PMC article


NeuroMaps (2010) is a Web-based application that enables investigators to map data from macaque studies to a canonical atlas of the macaque brain. It currently serves as an image processor enabling them to create figures suitable for publication, presentation and archival purposes. Eventually it will enable investigators studying any of several species to analyze the overlap between their data and multimodality data mapped by others. The purpose of the current project was to incorporate the Waxholm canonical mouse brain (Harwylycz, 2009) into NeuroMaps. An enhanced gradient echo (T2*) magnetic resonance image (MRI) of the Waxholm canonical brain (Johnson et al., 2010) was warped to bring the irregular biological midplane of the MRI into line with the mathematically flat midsagittal plane of the Waxholm space. The left hemisphere was deleted and the right hemisphere reflected to produce a symmetrical 3D MR image. The symmetrical T2* image was imported into NeuroMaps. The map executing this warp was applied to four other voxellated volumes based on the same canonical specimen and maintained at the Center for In-Vitro Microscopy (CIVM): a T2-weighted MRI, a T1-weighted MRI, a segmented image and an image reconstructed from Nissl-stained histological sections of the specimen. Symmetric versions of those images were returned to the CIVM repository where they are made available to other laboratories. Utility of the symmetric atlas was demonstrated by mapping and comparing a number of cortical areas as illustrated in three conventional mouse brain atlases. The symmetric Waxholm mouse brain atlas is now accessible in NeuroMaps where investigators can map image data to standard templates over the Web and process them for publication, presentation and archival purposes:


Figure 1
Figure 1. Edgewarp Screen Mockup
Left panel: midline sagittal section of Waxholm canonical mouse brain MRI showing vertical and horizontal axes through the origin of the Waxholm space in NeuroMaps. Plus sign (+) represent the locations of registration points used to flatten the biological midsagittal plane to the stereotaxic midsagittal plane; thin arrow: registration point illustrated in right panel; thick arrow: registration point added to correct the first warp (Sec. 2.2.7). Right panel: coronal section with two upper and two lower registration points recorded; cross-hairs illustrate recording of a fifth registration point.
Figure 2
Figure 2
Irregular shape of biological midsagittal plane of the Waxholm canonical mouse brain. The left-right (I) axis is scaled at 15-times that of the J- axis and about 4 times that of the K-axis to emphasize the pattern of deformation in different regions before flattening to the midsagittal plane of Waxholm space.
Figure 3
Figure 3. Symmetrical canonical brain
The result of flattening the midline and reflecting the right hemisphere to create a symmetrical canonical brain. Pictured are horizontal sections through the midpoint of the anterior commissure, vertical level j = 253 in the canonical Waxholm space using MRIcro (Rorden, 2010).
Figure 4
Figure 4
Cortical areas from three mouse brain atlases mapped to the symmetric Waxholm brain. Areas from Atlases A and B were mapped to the true coronal plane 0.02 mm rostral to the origin of the stereotaxic space, i.e., center of the anterior commissure (ac +0.02mm). The nearest comparable page of Atlas C was mapped to the NeuroMaps plane ac −0.17mm, top tipped forward 6°.

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