For ease of calling up images over the Internet at today's limited bandwidth, the atlas has been divided numerically into twelve broad regions each of 1000 microns length, and a pair of sections at 100 micron intervals through the entire brain is presented . Thus, almost all named structures are represented in the images. The nomenclature matches that in the paper atlas, with some additional or alternative names from more recent publications. The user has the option of choosing English or Latin nomenclature. All histological processing methods introduce distortions of brain tissue.
All images are in alignment, and absolute dimensions are readily recorded.
Warping of our histological images to an MRI series from brains of mice of the same strain, age and sex are currently in progress. The critical factors are alignment of section images and matching of stain intensities, because their precision controls the efficiency and accuracy of 3D segmentation. The 10 micron images have been aligned semiautomatically with newly written VoxelMath software, followed by small further manual adjustments using pixel-based visual landmarks. Based on beta tests carried out in recent months, a further refinement is anticipated later this autumn, when Bitplane's Autoaligner 2.0 software will be released. Differences in staining intensity from section to section may be hardly noticeable when one studies sections in the standard manner, but the differences become very important during 3D reconstruction.