To register your data, you will need a whole-brain image, i.e. not a part of a brain, and not some individual 2D sections. The format doesn't matter, as long as it can be loaded into napari, and the orientation etc. is dealt with by brainreg.
Loading your data into napari will vary depending on the data type, but with most types, you should be able to drag and drop your data into the main napari window.
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.
Choose the napari image layer you wish to be registered from
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).
These parameters are the same as the brainreg command-line interface. For more details on these, see the documentation here.
You can then click
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:
INFO - MainProcess cli.py:230 - Finished. Total time taken: 0:00:29.15
This means that the registration is complete, but you should see the results appear in the napari window.
Once the registration is complete, some new image layers will appear:
Atlas annotations - this the annotations image from the atlas (where each brain region has a unique value) warped to the data
Boundary image - this is a binary image, showing the boundaries between atlas regions.
These files are not the only ones created, they will all be saved in the output directory. These can be loaded into napari at any time, see the main visualisation page.