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TRACER: a toolkit to register and visualize anatomical coordinates in the rat brain

The need for anatomical registration and visualization tools is greater than ever thanks to novel technologies that allow users to record from thousands of neurons across multiple brain regions simultaneously. The vast majority of digital reconstruction toolkits for rodent models were developed using mouse brain atlases, leaving few options for those using rats. Retrofitting rat atlases into extant software is possible, but this demands effort and programming skills which most end-users lack. We therefore developed an open-source, python-based Toolkit for Reconstructing Anatomical CoordinatEs in Rats, TRACER, which allows users to reconstruct the trajectories of recording electrodes (e.g Neuropixels) or to visualize virus expression or other features in a comprehensively annotated 3D volume, the Waxholm Space (WHS) rat brain atlas. The WHS atlas is made from high-resolution magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI) scans, and contains >200 regional delineations. Beyond post-hoc reconstructions of electrodes or virus expression, TRACER can be used to generate coordinates for targeting brain regions prior to surgery. TRACER is available openly on GitHub and is compatible with Windows, macOS and Linux operating systems.