Plugins
at 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).Image layer
.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: