Visualising brainreg output#
If you have used the brainreg command-line interface, or simply want to view results at a later time, brainreg comes with a plugin for napari to allow you to easily view registration results.
Typically, you would view the results in sample space, i.e. with registration results overlaid on your data.
To begin, open napari and drag your brainreg output directory (the one with the log file) onto the napari window.
Various images should then open, including:
Registered image- the image used for registration, downsampled to atlas resolution
allen_mouse_25umthe atlas labels, warped to your sample brain
Boundaries- the boundaries of the atlas regions
If you downsampled additional channels, these will also be loaded.
Some of these images will not be visible by default. Click the little eye icon to toggle visibility.
N.B. If you use a high-resolution atlas (such as
allen_mouse_10um), then the files can take a little while to load.
napari-brainreg also comes with an additional plugin, for visualising your data in atlas space,
i.e., where your data is warped to the atlas coordinate space.
This is typically only used in other software, but you can enable it yourself:
Plugin Call Order
Plugin Sorterwindow, select
select hook...dropdown box
brainreg_read_dir_standard_space(the atlas space viewer plugin) above
brainreg_read_dir(the normal plugin) to ensure that the atlas space plugin is used preferentially.