Stack of books written by George Paxinos

Construction of a web-based 3D mouse brain atlas

Prof. Paxinos and Dr Schofield have produced very high resolution images of the adult and postnatal day 6 mouse brain at 40 micron intervals in 3 planes of section corresponding to The Mouse Brain in Stereotaxic Coordinates (Paxinos and Franklin, 4th Edition, Academic Press, San Diego, 2013) (Fig 1 and Fig 2). Prof. Susumu Mori and Jaymin Patel, collaborators at John’s Hopkins University, will use a population-based MRI/CT 3D atlas as a master high-anatomical-fidelity atlas to register the serial sections created in the Paxinos laboratory in all three directions. The registration parameters for matching each histology section to the master coordinates was established, and then each histology coordinate was linked to the 3D master atlas based on the labels in The Mouse Brain in Stereotaxic Coordinates (Paxinos et al., 2013). The Mori laboratory is developing a web-based interface ( to deploy these rich histological data with about 1,000 sections (each about 1GB) for users to explore the neuroanatomy in a 3D space.