We accelerate neuroscientific discovery by automating comprehensive mapping of neuronal activity, axonal projections, and biomarkers throughout mouse brains. We develop and operate analytical tools to process large 3D images of mouse brains captured via immunofluorescent labeling, tissue clearing, and light sheet fluorescence microscopy. For example, a single brain-wide image with cellular resolution is ~80GB in size and contains ~20 billion voxels, adding up to several terabytes of raw and analyzed data for each experiment. Similar to fMRI scans, the resulting maps highlight focal differences between experimental conditions, guiding mechanistic investigations targeting identified brain regions of interest.