The Neuroterrain 3D Mouse Brain Atlas

Abstract

A significant objective of neuroinformatics is the construction of tools to readily access, search, and analyze anatomical imagery. This goal can be subdivided into development of the necessary databases and of the computer vision tools for image analysis. When considering mesoscale images, the latter tools can be further divided into registration algorithms and anatomical models. The models are atlases that contain both bitmap images and templates of anatomical boundaries. We report here on construction of such a model for the C57BL/6J mouse. The intended purpose of this atlas is to aid in automated delineation of the Mouse Brain Library, a database of brain histological images of importance to neurogenetic research.

Keywords: 3D reconstruction; atlas; automated segmentation; brain model; neuroanatomy; registration; spatial normalization; standard coordinate space.

Figure 1

Sectional views through the NMBA. The initial cutting plane during generation of the sectional material was horizontal (A). The accuracy of the reconstruction can be appreciated from orthogonal resamples of the 3D volume along the coronal (B) and sagittal (C) planes and in the higher magnification views in (D) taken from (A–C). The smoothness of features such as the cell rich granular layer of the dentate gyrus (arrow in D) and of the pyramidal layer of the hippocampus (arrowhead in D) in all planes of view is indicative of effective registration. Note that application of gray value normalization has resulted in uniform staining intensity in all planes.

Figure 2

Surface views of NeuroNames level 1–3. Level 1 (A), the coarsest level, subdivides the CNS into brain (red) and spinal cord (green). The brain is further divided in level 2 (B) into forebrain (green), midbrain (yellow), and hindbrain (blue). In level 3 (C), the divisions are telencephalon (orange), diencephalon (pink), tectum (yellow), metencephalon (purple), and medulla oblongata (light blue).

Figure 3

Fine structure delineations. Shown are selected horizontal atlas levels with full delineation of the hippocampus (A) and olfactory bulb (B). Outline colors in (A): CA1 to CA3 represented in different values of blue; dentate gyrus (DG) – pink; fasciola cinereum-gold; granule layer of DG-red; hippocampal fissure-purple; molecular layer of DG-orange; oriens layer of the hippocampus-yellow; parasubiculum-green; polymorph layer of DG-pink-purple; presubiculum-light green; pyramidal cell layer of the hippocampus-dark baby blue; striatum radiatum of the hippocampus-light forest green; subiculum-green. Outline colors in (B): Accessory olfactory bulb (OB) and anterior olfactory nucleus-light green value; Dorsal lateral olfactory tract-turquoise; ependyma and subependymal layer of ventricle of OB-light lime green; external plexiform layer of OB and accessory olfactory bulb (AOB)-yellow-gold; glomerular layer of OB-dark green and of AOB-yellow-green; granule layer of AOB-blue; granule cell layer of OB-yellow; internal plexiform layer of OB-orange; lateral olfactory tract-green; mitral cell layer of OB-red; mitral cell layer of the AOB-light turquoise; olfactory nerve layer-red.