Detailed methodology for producing the rat brain atlas is provided in the first three editions (Swanson, 1992 , 1998 , 2004 ) that are available as open access legacy resources (Swanson, 2015b ) at larrywswanson.com . Briefly, after many attempts (starting in 1974) to obtain a complete series of transverse histological sections suitable for an atlas, one was obtained in 1982 from a 315‐g adult male Sprague‐Dawley rat that had been perfused with 4% paraformaldehyde and embedded in celloidin to hold separate parts of sections in place during mounting. All procedures for rats complied with NIH and institutional guidelines current from 1974 to 1982; the work on the atlas brain was done at the Salk Institute for Biological Studies, La Jolla, CA. Every section through the brain was collected, stained, and mounted; the first 133 sections through the olfactory bulbs were 30 µm thick, whereas the last 423 sections through the rest of the brain were 40 µm thick. The sections were stained with thionin and covered with DPX.
Because celloidin‐embedded tissue shrinks considerably and differentially in the rostro‐caudal, medio‐lateral, and dorso‐ventral dimensions, two Cartesian coordinate systems for the sections were produced. The first is a strictly physical coordinate system, corresponding to dimensions in the tissue sections themselves. The second is a stereotaxic coordinate system that ideally would be based on the dimensions of the brain within the skull of the intact, living animal. Fortunately, this brain was cut in virtually the same transverse plane as the stereotaxic rat brain atlas of Paxinos and Watson (1986), based on unembedded, frozen‐sectioned brains that suffered very little shrinkage. Because researchers have found the stereotaxic coordinates in Paxinos and Watson (1986) to be the best available, they were adopted for our brain as the second set of coordinates.
Photomicrographs of selected histological sections were obtained by placing the sections in an Omega enlarger with a point light source, projecting an image of the section onto a 4 × 5 inch sheet of Kodak Kodalith Ortho (2556) film, developing the film in Kodak Kodalith fine line developer, and printing with a Durst enlarger and Schneider Kreuzanch Componon‐S lens (f/150 mm) on 11 × 14 inch sheets of Kodak Kodabrome II RC paper, contrast grade F5. After 35 years, these thick celloidin sections are unsuitable for high resolution digital scanning because they are not completely flat and because the DPX has retracted in places, creating random “bubbles” of air between tissue section and coverslip. However, most areas of the sections remain suitable for microscopic examination.
Because celloidin‐embedded tissue shrinks considerably and differentially in the rostro‐caudal, medio‐lateral, and dorso‐ventral dimensions, two Cartesian coordinate systems for the sections were produced. The first is a strictly physical coordinate system, corresponding to dimensions in the tissue sections themselves. The second is a stereotaxic coordinate system that ideally would be based on the dimensions of the brain within the skull of the intact, living animal. Fortunately, this brain was cut in virtually the same transverse plane as the stereotaxic rat brain atlas of Paxinos and Watson (1986), based on unembedded, frozen‐sectioned brains that suffered very little shrinkage. Because researchers have found the stereotaxic coordinates in Paxinos and Watson (1986) to be the best available, they were adopted for our brain as the second set of coordinates.
Photomicrographs of selected histological sections were obtained by placing the sections in an Omega enlarger with a point light source, projecting an image of the section onto a 4 × 5 inch sheet of Kodak Kodalith Ortho (2556) film, developing the film in Kodak Kodalith fine line developer, and printing with a Durst enlarger and Schneider Kreuzanch Componon‐S lens (f/150 mm) on 11 × 14 inch sheets of Kodak Kodabrome II RC paper, contrast grade F5. After 35 years, these thick celloidin sections are unsuitable for high resolution digital scanning because they are not completely flat and because the DPX has retracted in places, creating random “bubbles” of air between tissue section and coverslip. However, most areas of the sections remain suitable for microscopic examination.
