Mouse Brain Atlas: C57BL/6J Coronal

Use the image below to select a section through the brain. The bregma zero coordinate is marked by the grey circle. Click on a button to view the corresponding section, or use the numbered guide in the frame below. Scroll down for more background on this atlas.

Navigation Map

The markers above are spaced 1 mm apart and correspond to levels of the Atlas. The zero coordinate is the bregma point, a landmark visible on the skull. To use this atlas effectively you may need to assign your browser more memory than usual. If you are connecting at 56K you will also need patience. Many of the jpeg-compressed images are 100K to 500K.

If you click on the buttons for "grid" or "labels" in the brain section area before the page finishes loading images, you may not be able to view the gridded or labeled images without reloading the page. JavaScript must be enabled to view the small versions of the gridded and labeled sections, but the enlarged images can be viewed with any settings. They are so large that you will need to use the scroll bars to view different parts of the image. You may want to copy pages of the Altas to your computer and then view them using a program such as Photoshop.

About this Atlas: The brain is that of a 51-day-old C57BL/6J male with a body weight of 20.2 gm and a brain weight (fixed) of 477 mg. The animal's celloidin case ID number is 170 and you can view one of the slides used to make this atlas. Shrinkage during fixation and processing is 25% (linear). The in vivo grid compensates for this shrinkage. The anterior-posterior coordinates are taken from an excellent print atlas of a C57BL/6J brain by K. Franklin and G. Paxinos (The Mouse Brain in Stereotaxic Coordinates, Academic Press, San Diego, 1997, ISBN Number 0-12-26607-6; Library of Congress: QL937.F72). The abbreviations we have used to label the sections conform to those in the Franklin-Paxinos atlas. A brain such as this one contains approximately 75 million neurons, 23 million glial cells, 7 million endothelial cells associated with blood vessels, and 3 to 4 million miscellaneous pial, ependymal, and choroid plexus cells (see data analysis in Williams, 2000)

The brain and sections were all processed as described in our methods section. The enlarged images have a pixel count of 1865 x 1400 and the resolution is 4.5 microns/pixel for the processed sections.

Plans: In the next several years we hope to add several additional atlases of the same sort for other strains of mice. A horizontal C57BL/6J atlas and a DBA/2J coronal atlas were completed by Tony Capra, summer 2000, and additional atlases may be made over the next several years. As describe in our MBL Procedures Section it is not hard to make your own strain-specific atlas from the high resolution images in the MBL.