Pluginsat the top of the main napari window, and then click
brainreg-register: Atlas registration. A new docked widget will appear in your napari window.
Image layer, along with the atlas you want to use from
Atlas. You must also set the voxel sizes in the axial (z) and in-plane (x, y) dimensions, along with the data orientation. The orientation is defined by three letters, based on bg-space, e.g.
psl. For more details on this, see the outline here. Lastly, set an
Output directory(where you want to save the data).
Run, and the registration will start. Lots of stuff will get printed to the console as brainreg runs, and when it's done (it should only take a minute or so), you will see something like: