The hardware requirements for brainreg depend on the atlas (and in particular, the resolution) you want to use. Most machines (including laptops) will be able to use most of the atlases, but some atlases (such as the 10μm mouse atlases) may need up to 50GB of RAM.


There are two ways to run the registration using brainreg. If you’re just getting started, we recommend the napari plugin. This provides a graphical user interface, and makes it easier to tweak parameters.

If you need to run brainreg on many samples, or on a remote machine (e.g., using an institutional high-performance computing system), there is a command-line interface.

Whichever interface you use, the results will be identical.

Download atlas (optional)#

When brainreg runs, the appropriate reference atlas will be downloaded (if not previously done so). To install download BrainGlobe atlases in advance, please see the guide to the BrainGlobe Atlas API command-line interface for details.