Visualisation

Usage
Sample space
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
atlas_name - e.g. allen_mouse_25um the 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.
Visualisation in sample space
Atlas space
napari-brainreg also comes with an additional plugin, for visualising your data in atlas space.
This is typically only used in other software, but you can enable it yourself:
Open napari
Navigate to Plugins -> Plugin Call Order
In the Plugin Sorter window, select napari_get_reader from the select hook... dropdown box
Drag 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.

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Usage

Sample space

Atlas space