User guide

Getting started
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 data
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. 
If you are having trouble loading your data into napari, first check the napari hub to see if there's a plugin to help. If that fails, go ahead and ask the nice people at the image.sc forum.
Starting the plugin
Click 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.
Setting up registration
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).
Make sure that the image layer you are registering is not selected in the list of napari image layers on the left hand side. Any images that are selected, will also be registered along with the image layer chosen in Image layer.
Setting additional parameters
These parameters are the same as the brainreg command-line interface. For more details on these, see the documentation here.
Running brainreg
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. For more details of the output files created, please see Output files.

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Getting started

Loading data

Starting the plugin

Setting up registration

Setting additional parameters

Running brainreg