Visualise an atlas in napari#
BrainGlobe atlases are made of different components. These include the annotations image, the (default) reference image, 3D atlas region meshes and, optionally, additional reference images. In this tutorial, you will use
brainrender-napari to visualise each of these components in the 3D viewer napari through a series of simple clicks. The
mpin_zfish_1um zebrafish brain atlas will serve as an example.
You will need
napari installed on your computer - please follow
napari’s installation instructions to do so.
Plugins > Install/Uninstall pluginsand searching for
brainrender-napariin the searchbox. Then click on the
brainrenderwidget by selecting
Plugins > Brainrender (brainrender-napari)in the napari menu bar near the top left of the window.
The brainrender widget appears on the right hand side of the window.
Atlas table viewsection, double-click the row which contains the
mpin_zfish_1umatlas (you may have to scroll down slightly).
You have now added the annotations image and the default reference image to napari: They appear as layers in the napari layers list on the lower left of the window. A
3D Atlas region meshes section appears below the
Atlas table view section.
If you haven’t downloaded the atlas before, the plugin will prompt you to download it (click yes). It may take a long time (depending on your internet speed) so please be patient. Once downloaded, double-click again to view the atlas.
Toggle the napari display from 2D to 3D by pressing the button with the square icon on the lower left of the window.
The annotations image should now be displayed in 3D.
6. Navigate the brain region tree in the
3D Atlas region meshes section by opening “forebrain”. Double-click on
You have now added a 3D atlas region mesh layer, which appears as a mesh in the viewer and as a new layer in the layers list.
7. Back in the “Atlas table view” section, right-click on the
mpin_zfish_1um row. In the menu that appears, select
You have now added an additional reference image, which appears as a grey scale image in the viewer and as a new layer in the layers list.
You have now added all possible kinds of BrainGlobe atlas components (annotations image, reference image, 3D atlas region mesh, additional reference) to napari - well done! You can now add any of the other atlases listed in the
Atlas table view if you like (note that not all atlases have additional references!).
Hover over any of the elements in the
brainrender widget to get additional hints about how to use them!