Registering a whole-brain image to an atlas#

In this tutorial, you will use the brainreg plugin for napari to register (align) a whole-mouse brain image to a reference atlas.

The focus of this tutorial is simply to successfully register a single image. Optimising brainreg for specific applications will be covered separately.


You will need napari installed on your computer - please follow napari’s installation instructions to do so.

  1. Open napari.

  2. Install brainreg-napari by selecting Plugins > Install/Uninstall plugins and searching for brainreg-napari in the searchbox. Then click on the Install button.

  3. Open the brainreg widget by selecting Plugins > Atlas registration (brainreg-napari) in the napari menu bar near the top left of the window. brainreg widget

The brainreg widget appears on the right-hand side of the window.

  1. Open the sample image by selecting File > Open Sample > Low resolution brain (brainreg-napari).

  2. Make the image easier to see by adjusting the contrast limits in the top left section of the napari window. Moving the right-hand slider to the left will make the image appear brighter. loaded image

A whole mouse brain image loaded into napari.

  1. In the plugin widget, set all the necessary parameters:

  • Image layer - Set this to the Sample brain image layer

  • Atlas - Set this to allen_mouse_50um

  • Data orientation - Set this to psl

  • Voxel size (z) - Set to 50

  • Voxel size (x) - Set to 40

  • Voxel size (y) - Set to 40

  • Output directory - Click Choose directory, and create a new directory on your machine

  1. Click Run. After 30-60 seconds, two new napari layers will be loaded, Boundaries and allen_mouse_50um.

  2. Toggle the visibility of these two layers (using the eye icon on the left of the layer name) to overlay the registration results. These can be explored by zooming in/out, scrolling through the 3D data and adjusting the visibility and contrast of the loaded data.

loaded image

Registration results overlaid onto raw data.

  1. At this point, registration is complete. A number of files are created in the output directory that can be used for downstream analysis.


The results are likely not perfect because (for speed and simplicity) we:

  • Used very low-resolution data

  • Use a low-resolution atlas

  • Left all the parameters as default (which were optimised for higher resolution atlases)


For full information on how to use brainreg, please see the brainreg page