Abstract
This is a full-color atlas of Nissl-stained fresh-frozen brain sections from 8-week-old male C57BL/J6 mice presented as a spiral-bound work with easy-to-turn, nonbinding pages. The author opens with a must-read preface describing the scope and mission of the atlas, which are, in the author's words, not only to provide a detailed cytoarchitectonic map that navigates brain structures, but also to serve as a key component of the Allen Brain Atlas gene expression database, which is an online accessible, three-dimensional map of gene expression in the mouse brain. The introduction (Section 1) gives a brief history of modern neuroanatomy and brain mapping, taking the reader through gross neuroanatomy and the development of cytoarchitectonics, myeloarchitectonics, and chemical, molecular, and computational neuroanatomy that have led to our current understanding of the spatial and functional organization of the brain. Section 2 describes the construction of the Allen Reference Atlas, basically a “materials and methods” section of how the images were produced. This is followed by a detailed description of the hierarchical organization of the mouse brain used in the atlas, which was modified from standard references to reflect functional and ontological differences found from in situ hybridization gene expression data generated in the author's lab. The hierarchy scheme was used to color code the annotated images in the atlas. The references in this section are very complete, and it is well worth reading for the novice neuroscientist and the seasoned veteran. Section 3 describes research applications of the atlas. Because the atlas is available in an online version (which is free), users can correlate gene expression data, also online, with the atlas images. The atlas was also used to make a vector-based three-dimensional computer graphics model that can be accessed through a free download; in this application, sections of the brain can be viewed via virtual cutting planes along any of the 3 major axes, or structures can be viewed in 3 dimensions.
Sections 4 and 5 of the atlas present beautiful, high-resolution, 24-bit color images of 25-μm thick, Nissl-stained sections spanning the entire mouse brain; there are 21 sagittal sections spaced 200 μm apart and 132 coronal sections spaced 100 μm apart. For coronal sections, the brain structures were drawn and annotated on one half of each image using Adobe® Illustrator® CS. Sagittal section images are presented in their entirety, with the correlating drawn and annotated image on the facing page. Each annotated image is color coded according to the hierarchical scheme described in Section 2. The coordinates from bregma and/or midline are presented on each page, along with a list of abbreviations used in the image (structure key) and a list of gene markers (by region in which they are expressed and by gene symbols) used in the in situ hybridization technique. One drawback is that the color codes for the hierarchy scheme are not presented on each page and must be memorized or looked up in a table at the back of the atlas. Sections 6 and 7 present lists of tables, most important of which is the hierarchy used in the atlas (basic cell groups and regions of the mouse central nervous system); strangely, this table does not include the color coding, but colors can be inferred from a schematic view presented in Section 2.
The atlas comes with a CD-ROM that contains PDF and jpeg files of the graphic images in the atlas; the images are black-and-white, non-Nissl drawings of the sections, which can be used for presentations and data mapping. The PDF files are much clearer at smaller magnification, and some of the lines do not appear in the jpeg files.
Overall, this atlas is an incredible compilation of work and is beautifully and artistically presented. The author clearly describes where this atlas differs from other published atlases, particularly with respect to differences in ontology and nomenclature. For the bench pathologist, it is an easy-to-use source for navigating the mouse brain. For the researcher, it is a tool, providing a framework on which to present and compare data, particularly because of the Web applications.