Command line interface

Although the atlases will be downloaded when you need them, we provide a command line interface to view which atlases are available, and update them if necessary.

To see the list of atlases available, run brainglobe list

To download an atlas, use brainglobe install , the -a flag, followed by the name of the atlas, e.g.:

brainglobe install -a allen_mouse_25um

To update an atlas to a newer version, use brainglobe update, e.g.:

brainglobe update -a allen_mouse_25um

Further instructions can be found by running brainglobe --help.

Hint

We also provide a graphical user interface to download and update atlases, as part of the brainrender-napari package.