Download an atlas through napari#

In this tutorial, you will use brainrender-napari’s Atlas Manager widget to download a BrainGlobe atlas through a series of simple clicks. The mpin_zfish_1um zebrafish brain atlas will serve as an example.

Note

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

  1. Open napari.

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

  3. Open the Atlas Manager widget by selecting Plugins > Brainrender > Manage atlas versions in the napari menu bar near the top left of the window. brainrender widget

The Atlas Manager widget appears on the right hand side of the window.

  1. In the widget’s Atlas Manager section, double-click the row which contains the mpin_zfish_1um atlas (you may have to scroll down slightly). 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.

Note

We are working on providing a progress indicator in napari - in the meantime, you can see download progress in the terminal from which you launched napari.

atlas manager dialog

You have downloaded the zebrafish atlas - you can visualise it in napari by following our atlas visualisation tutorial.