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The Brain Atlas and Stereotaxic

brain sliceYou wake up one morning and decide you’re going to take a trip. You get a destination in mind, hop in your car and start to drive, only to realize you have no idea how to get there. Just as you wouldn’t leave to go on a trip without researching your destination first, so too should a researcher know how to find their ultimate destination before starting their work. The brain atlas is the first resource that should be used to determine how to find this location.

What is an Atlas?

A brain atlas is a roadmap to basic brain structures. The first rat brain atlas, The Rat Brain Coordinates in Stereotaxic, was published by Paxinos and Watson in 1982. The book is currently in it’s 7th edition (2014) and is considered one of the most trusted resources of neuroscience researchers.

An atlas is comprised of photos or diagrams of brain slices done at set intervals. This interval ranges anywhere between 100 - 200 Micrometre in thickness. The diagrams can be shown in either coronal or sagittal sections. This layering helps form a 3D version of the brain which allows the researcher to pinpoint their structure of interest with a higher degree of accuracy. Particular structures of interest to researchers performing infusions in rodents include third ventricle, nucleus accumbens, amygdala, VTA, substantia nigra, hippocampus, prefrontal cortex and cerebrum. These brain structures would each be marked in the atlas.

Structures are given location designations, called coordinates, which specify where the structure is normally found in the brain. The coordinates are oriented around bregma, which is the joining point of the skull bones, and is easily identifiable during surgery. The coordinates are calculated in three planes: anterior/posterior, medial/lateral and dorsal/ventral. Each point would be calculated distance from bregma.

Once the researcher has determined their coordinates from the atlas, these are entered into their stereotaxic equipment before the surgery.

What is a stereotaxic and how does a stereotaxic work?

A stereotaxic frame provides a surgical stage, in both humans and research animals surgeries. Stereotaxic surgery requires stability and fixed points of reference in order to plot the coordinates correctly and ensure a successful implantation. The structure and shape of the skull makes it an ideal candidate for stereotaxic surgery.

The basic components of a stereotaxic are a frame, calibrated coordinate adjustment dials, manipulator arms, ear bars, incisor/nose bar and a cannula, electrode or microdialysis mounting holder.

Most often found in a "C" or "U" shape, the frame has a myriad of customization options based on what best fits the application of the researcher. For example, researchers targeting multiple sites may choose frames that hold several manipulator arm attachments.


The ear bars and incisor/nose bar are used to fix the animals position before and during the surgery. The ear bars gently hold the animals head in a flat, neutral position so that the researcher can easily access the top of the animals head. The incisor/nose bar holds the snout in place and allows for small adjustments in angle of the animals head.

The manipulator arms and the mounting holder work in conjunction to allow precise placement of cannula or electrode. The arms have a clamping mechanism which allows them to hold a variety of attachments based on whatever application may be needed. The mounting holder fits into the manipulator arm and holds the object for placement during the surgery.

There are several reputable companies selling stereotaxic equipment and frames including Kopf, Stoelting and BASi. Plastics One is proud to offer a line of mounting holders compatible with these and others stereotaxic equipment.

The internet has given rise to more interactive atlas models, which allow the user to move and scale the brain with ease. The future of brain structure mapping and data sharing makes it an exciting time to be in research.

Contact us today for more information or for a customized solution for your project!