The same dorsal plane is shown from (a) CT1, (b) CT2, and (c) CT2* with each different acquisition highlighting different cytoarchitecture.

The same dorsal plane as shown in Figure 1 is displayed with (a) the matching Nissl volume; (b) CT2*; and (c) CT2* with labels superimposed. There is good correspondence between the Nissl and CT2* image.

A dorsal slice from MLA shows the maximum likelihood labeling for each pixel in the image. Pixels are color-coded, so the color defines the structure for which the pixel has the highest probability. The shading of the colors depicts the fact that the maximum probability at the boundary between structures decreases as one moves across the boundary.

All the MR data are isotropic. Thus, there is no loss of resolution between (a) the coronal plane and (b) the sagittal plane of CT2*. The color labels superimposed in (a) and (b) can be seen as transparent surfaces demonstrating the 3D juxtaposition of structure in the volume rendered image in (c). The key for the labels is included in Table 2.

CT1 is shown texture-mapped on to orthogonal slicing planes. The light-blue color overlay is the label for the whole brain. The blue-orange-yellow color overlay is an Allen Brain Atlas gene expression correlation map (AGEA: http://mouse.brain-map.org/agea) rendered by maximum intensity projection. The AGEA seed voxel was chosen in Waxholm Space by navigating CT1 to a subfield where the hippocampus is clearly visible. The coordinates were transformed to Allen Brain Atlas (ABA) space, the corresponding correlation volume requested from the ABA web service, and the returned volume transformed back to Waxholm Space for viewing. (Courtesy of Chris Lau, Allen Brain Institute)

As new types of MR data become available, they can be efficiently mapped into WHS through the use of an alignment protocol, i.e. a dataset acquired with either LoResT1 or LoResT2* (Table 1). The T2*-weighted image in (a) was acquired prior to the acquisition of the multiple scans required for calculating diffusion tensor imaging (DTI)—see (Jiang and Johnson, 2010). The DTI data in (Jiang and Johnson, 2010) was aligned to WHS, thus expanding the space with the inclusion of (b) fractional anisotropy and color-coded eigenvalues. The low-resolution gradient-recalled echo (GRE) protocol (LoResT2* - Table 1) can be acquired in < 1 hour.

The high contrast-to-noise-ratio provided in the average images: (a) AT1, (b) AT2, and (c) AT2* allow identification of a number of structures. Granule cell layers stand out in AT1 and AT2* as dark regions in the olfactory bulb (GrO - granular olfactory bulb, GrA - granular accessory olfactory), and hippocampus (GrDG - granular dentate gyrus). In contrast to GrDG, the pyramidal cell layer (Py) of the hippocampus appears less hypointense. A distinction between the CA1 (hypointense) and CA3 (hyperintense) areas of the hippocampus is most evident in the AT2*, but can also be seen in the AT1. White matter fibers such as fimbria (fi), fornix (f), fasciculus retroflexus (fr), internal capsule (ic), and stria medullaris (sm) are identified easily in the AT1. The mammillary tract is visible in the AT2. Thalamic (IAD - interanterodorsal, Rt - reticular, SG - suprageniculate, VG - ventral geniculate, DLG - dorsal lateral and IGL intrageniculate lamina) and hindbrain (MVE - medial-vestibular and LVE - lateral-vestibular) nuclei are best seen in AT2, as well as the nuclei of the lateral lemniscus (VLL - ventral nuclei of the lateral lemniscus) the accessory olfactory bulb (AOB). TRS - triangular septal nucleus, however, is best seen in the T2s. Differences in cell types, density, and myelination identify distinct areas of the cortex such as ENT- the entorhinal cortex, and individual layers, such as EPl - the external plexiform layer, MI - mitral cell layers in the olfactory areas, or Layer IV in the neocortex.