AtlasGuide: software for stereotaxic guidance using 3D CT/MRI hybrid atlases of developing mouse brains

Stereotaxic operations of the mouse brain are critically important for various types of neuroscience research studies, which include electrical recording of neural activities or site-targeted injection of stem cells, chemical tracers, and vectors, to name a few. To guide such operations, two-dimensional histology-based mouse brain atlases, such as the Paxinos and Franklin atlas, are widely used. Recently, computed tomography (CT) and magnetic resonance imaging (MRI) based hybrid three-dimensional (3D) atlases of developing mouse brains have been introduced. In this study, a new stereotaxic guidance software, called AtlasGuide, is introduced, which was developed to fully utilize the benefits of the 3D atlases for high-precision stereotaxic targeting. The AtlasGuide software provides functions to visualize oblique needle paths in 2D and 3D views, which allow investigators to simultaneously examine brain structures that could be damaged by the needle path and optimize the injection angles for high-precision trajectory selection through critical neural tissue. It allows reorientation and scaling of the atlases dynamically to match the orientation of the animal brain prepared for surgery, thereby eliminating the need to manually align the subject to the atlas, a procedure which is essential while using conventional 2D atlases. In addition, the software enables loading user-defined atlases when researchers need image-based guidance for different age groups, strains, or species. The software with integrated 3D stereotaxic mouse atlases is available for download at the http://lbam.med.jhmi.edu website.