A three dimensional (3D) computerized map of rat brain anatomy created
with digital imaging techniques is described. Six male Sprague-Dawley
rats, weighing 270-320 g, were used in the generation of this atlas.
Their heads were frozen, and closely spaced cryosectional images were
digitally captured. Each serial data set was organized into a digital
volume, reoriented into a flat skull position, and brought into regist
er with each other. A volume representative of the group following reg
istration was chosen based on its anatomic correspondence with the oth
er specimens as measured by image correlation coefficients and landmar
k matching. Mean positions of lambda, bregma, and the interaural plane
of the group within the common coordinate system were used to transfo
rm the representative volume into a 3D map of rat neuroanatomy. Images
reconstructed from this 3D map are available to the public via Intern
et with an anonymous file transfer protocol (FTP) and World Wide Web.
A complete description of the digital map is provided in a comprehensi
ve set of sagittal planes (up to 0.031 mm spacing) containing stereota
xic reference grids. Sets of coronal and horizontal planes, resampled
at the same increment, also are included. Specific anatomic features a
re identified in a second collection of images. Stylized anatomic boun
daries and structural labels were incorporated into selected orthogona
l planes. Electronic sharing and interactive use are benefits afforded
by a digital format, but the foremost advantage of this 3D map is its
whole brain integrated representation of rat in situ neuroanatomy.