Although the AAL and Brodmann atlases were popular, they might perform more poorly than other atlases, such as the LPBA40 [22].
The existing (commercially available) brain atlases, such as ADAM [6], Cerefy [7], Digital Anatomist [8], and Voxel-man [9], are anatomically incomplete; moreover, besides our Cerefy atlases [10], none of these atlases has been used in clinical applications.
The conceptual surface-based atlases provide an interesting and useful way to index, browse, visualize, and digest slice-based atlases and may prove to be a valuable complement to standard atlases such as [12].
For particular "model organisms" extensive online documentation (including embryology) is already available, such as the Edinburgh mouse atlas project, the Xenopus-, C. elegans- or Drosophila-project (e.g. summarised by Bio-Ontologies [89]).
Many other spatial gene expression patterns generated via RNA ISH such as FlyBase (Drysdale, 2008) and Mouse Atlas (Lein et al., 2006) provide rich information for genetics.
The co-ordinates of the clusters were reported according to the conventional Lambda-Bregma system in the Allen Mouse Atlas (http://mouse.brain-map.org/atlas/index.html).html
Seriation was conducted on simulated, retinal or Mouse Atlas SAGE data using the custom MATLAB implementation.
MAPaint software, developed by the Edinburgh Mouse Atlas Project [32] [34], was used to analyze these vacuoles.
Another example of a mouse atlas that provides gene expression data for the mouse brain is the GENSAT brain atlas.
At alternate sections, the boundaries of the hippocampus were determined using the stereotaxic mouse atlas [20].
