The stereotaxic approach of a target structure in the rodent brain requires sufficient theoretical knowledge on the specific locations of different brain regions. The stereotaxic atlas, a necessity in stereotaxic procedures, provides the layout of the rodent brain through theoretical coordinates for the implantation of cannulae, electrodes, and other instruments.

Given that an important element of the stereotaxic procedure is the accurate quantification of internal and external distances in preparation for rodent surgery, stereotaxic atlases provide the precise coordinates for particular brain regions along the three orthogonal planes. The three adjustable vernier screwdrivers in the stereotaxic apparatus, which deliver accurate quantification of distances, are moved along these three planes, namely–the anteroposterior (AP) axis, running from the anterior to the posterior part of the animal’s head; the mediolateral (ML) axis, running along the midline to the right or left side; and the dorsoventral (DV) axis, running from the surface of the skull to the brain’s interior.

In targeting particular brain structures, these stereotaxic coordinates given along the anteroposterior, mediolateral, and dorsoventral planes are calculated with respect to two distinct reference points on the surface of the animal’s skull; the bregma and lambda. It is the researcher’s responsibility to choose the appropriate reference point based on the target structure’s location. Usually, the closest reference point to the target structure is chosen. For instance, if the target structure is the hippocampus, the bregma may be recommended as a landmark as opposed to the lambda.

Many stereotaxic atlases have been published, each catering to differences in rodent species as well as animal body weight, sex, strain, and age. It is, therefore, the researcher’s responsibility to take all of these principal factors into consideration in the preliminary process of choosing the appropriate reference material for the duration of the experiment. It should be noted that stereotaxic atlases do not necessarily use the same cartographic parameters, and in using multiple atlases, one must use parameters valid only for the particular material. Cited below are some of the rodent stereotaxic atlases that have been in use by researchers since the advent of stereotaxic surgery. The different authors of these atlases have provided infinitely beneficial reference tools, with different features that serve specific purposes.

Stereotaxic Surgery in the Rat: A Photographic Series
Cooley and Vanderwolf’s (2nd ed, 2005) Stereotaxic Surgery in the Rat: A Photographic Series offers clear, simple, and step by step outlines of the procedures involved in stereotaxic surgery. This book is considered a perfect tool for novice and student use, as it provides basic information alongside extremely high-quality photographs of the rat brain. Though the book may not have extremely specific tags and labels, it compensates with the quality of visual presentation, a highly useful criterion for those who are just starting out in the field.
The Cortex of the Rat: A Stereotaxic Atlas
Beyond providing a general guide for navigating the rodent brain, some atlases place more focus on specific areas and structures. The Cortex of the Rat: A Stereotaxic Atlas by Zilles (1st ed, 1985). This atlas provides information on the delineation of cortical areas in the rat brain as a guide for experimental procedures involving these structures.
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Atlas of Prenatal Rat Brain Development
More specific atlases of the rat brain also outline structures at different stages of development. One such publication is Altman and Bayer’s (1994) Atlas of Prenatal Rat Brain Development, which is a comprehensive atlas of the developing rat brain as presented in both coronal and sagittal sections. Because the prenatal rodent brain is composed of highly fragile anatomy that can be enormously challenging to work with, Altman and Bayer’s work is a welcome tool in navigating the prenatal structures, which are vastly different from the adult rodent brain. Studying the prenatal brain has allowed researchers to gain a deeper understanding of the development of the brain, with regard to malfunctions and abnormalities.
Brain Maps: Structure of the Rat Brain
Swanson’s (3rd ed, 2004) Brain Maps: Structure of the Rat Brain was a stereotaxic atlas for rat surgery that was made available to the public as an open-access atlas. The material includes downloadable artwork and Adobe Illustrator files for editing, as well as an accompanying discussion of stereotaxic methods and procedures. Given that it is open for public use, Swanson's work is a beneficial contribution to the field of stereotaxy for researchers who can't yet spend much on expensive and up-to-date atlases. More than that, the Brain Maps series also caters to the modern and digital age of scientific research, and can be an infinitely useful tool for those who are more inclined to use the highly technological software in the laboratory, instead of traditional means. Swanson's work can be considered part of a larger trend in science, technology, and society that sees us moving and progressing towards a more digital and interconnected plane of professional work. Using Swanson's software has implications for the ease of use and wide-reaching sharing abilities of such manuals. Brain Maps also gives its users the ability to engage with the product through easy manipulation and illustration on top of the diagrams.
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Rat Brain in Stereotaxic Coordinates
The Rat Brain in Stereotaxic Coordinates (7th ed, 2013) by Paxinos and Watson can be considered the most widely-used and trusted source of stereotaxic coordinates and anatomical information of rats by researchers today. The level of specificity and detail, clarity of photographs and drawings of coronal, horizontal, and sagittal sections, as well as the usage of modern histochemistry techniques involved in producing this publication, makes it the most accurate stereotaxic atlas to date. Digital advances in technology have also introduced the use of electronic diagrams, which have also been made available with a purchase of this stereotaxic atlas.

Stereotaxic Atlases for the Mouse

  1. Atlas of the Mouse Brain and Spinal Cord & Stereotaxic Atlas of the Diencephalon and Related Structures of the Mouse

The earliest material made available for stereotaxic procedures on the mouse was Sidman, Angevine, and Taber’s (1971) Atlas of the Mouse Brain and Spinal Cord, and Montemurro and Dukelow’s (1971) Stereotaxic Atlas of the Diencephalon and Related Structures of the Mouse. These two books paved the way for the development of more reference materials for stereotaxic surgery in mice.

Web-Based Allen Brain Atlas of the Mouse

  1. The Allen Brain Atlas is a mouse brain anatomical atlas and gene expression database that’s made available online. This online reference tool includes both coronal and sagittal views of the mouse brain, presented as full-color plates with corresponding labels and genetic markers. This digital color brain atlas of the mouse brain is great reference material for researchers and scientists, and one of the best features of this stereotaxic atlas is how different brain structures are visually organized by assigning different color hierarchies to each area. The use of color hierarchies is also a huge advantage in the computer-generated 3D reconstruction of the mouse brain.
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Prenatal Mouse Brain Atlas
Just like prenatal brain development in rats, some authors of stereotaxic atlases for mice have also come up with a much-needed guide for prenatal brain structures. The Prenatal Mouse Brain Atlas by Schambra (2008) is the only comprehensive atlas guide available for studies on the early embryonic to late fetal stages of the mouse brain. It provides sectional views of the mouse brain across four different stages, particularly, gestational days 12, 14, 16, and 18, while also highlighting specific areas of developmental interest. This particular reference tool carries color images of whole, hematoxylin, and eosin stained sagittal, coronal, and horizontal sections.
Mouse Brain in Stereotaxic Coordinates
Today, the most reliable mouse stereotaxic atlas comes from one of the same authors for the rat stereotaxic atlas, Paxinos and Franklin (4th ed, 2012) with the Mouse Brain in Stereotaxic Coordinates. This particular publication provides the international standard for stereotaxy in mice, with high-quality microscopic plates in full color and fully updated coronal and sagittal diagrams. Similar to the pioneer stereotaxic atlas for the rat, this reference tool for mice also comes with a CD of all plates and diagrams, as well as Adobe Illustrator files, making learning and manipulation easier with the available digital technology today. For most scientists and researchers, Paxinos’ work in rodent stereotaxy is as reliable as one can hope to be and has therefore been the most trusted source of reference materials for stereotaxy for years.