DMC-BrainMap - an open-source, end-to-end tool for multi-feature brain mapping across species

A central goal of current neuroscience research is to understand how behavior emerges from neuronal circuit activity. For this, cellular and circuit components in intact brains need to be identified and studied using e.g. viral tracing, electrophysiology, imaging, activity perturbations, and behavior. A commonality of these approaches is the need to establish the anatomical locations of both experimental parameters (e.g. recording/injection sites) and circuit components (e.g. cell bodies/projections). The development of standardized coordinate systems, i.e. reference brain atlases, has proven essential for reproducible, cross-laboratory mapping of anatomical data. However, the process of mapping, analyzing, and visualizing anatomical data remains challenging, especially for users lacking programming expertise. Here, we introduce DMC-BrainMap, an open-source napari plugin designed as a user-friendly tool for streamlined processing and whole-brain analysis of anatomical data. The working principle and core functionalities include all steps after image acquisition, i.e., preprocessing of images, registration of images to a reference atlas, segmentation of different anatomical features, and data analysis/visualization. DMC-BrainMap can be applied to histological data obtained from a variety of model organisms at different developmental stages, including mouse, rat, and zebrafish. We demonstrate the utility of DMC-BrainMap by mapping and quantifying cell bodies, axonal densities, injection sites as well as placement of optical fibers and Neuropixels probes. Further, we show how spatial transcriptomics data can be integrated into the DMC-BrainMap workflow. By eliminating the need for programming by the user, DMC-BrainMap provides an easy-to-use tool for increased rigor, reproducibility, and data sharing in neuroscientific research involving animal models.