Segmenting 2/3D structures#

In this tutorial, you will use the brainglobe-segmentation plugin for napari to segment a a 3D (or 2D) structure, such as an injection site. As a prerequisite, you will need to have registered your data to an atlas using brainreg and know what folder you saved this in (your “brainreg output directory”). If you don’t have this, please follow our registration tutorial first.


You will need napari installed on your computer - please follow napari’s installation instructions to do so (including their recommendation to use a conda environment).

  1. Open napari.

  2. Install brainglobe-segmentation by selecting Plugins > Install/Uninstall plugins and searching for brainglobe-segmentation in the searchbox. If it is not installed yet, click on the Install button.


On Silicon Macs you may have to conda install hdf5 first for the installation to be successful.

  1. Open the brainglobe-segmentation widget by selecting Plugins > Region/track segmentation (brainglobe-segmentation) in the napari menu bar near the top left of the window. The brainglobe-segmentation widget appears

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

  1. Load your registered data in atlas space by clicking on Load project (atlas space) and navigating to your brainreg output directory.

  2. If required, adjust the contrast on the registered image by selecting the Registered Image layer on the left of the screen, and clicking on Autocontrast: once on the top left of the screen.

  3. Click the Region Segmentation button in the Segmentation panel.

  4. Click the Add new region button.

A new Labels layer appears

A new Labels layer named region_0 appears on the left hand side.

  1. If required, rename this region (by selecting the e.g. region_0 text)

  2. Navigate to where you want to draw your region of interest.

  3. Choose a brush size (top left box).

  4. Make sure painting mode is activated (by selecting the paintbrush icon, top left). You can go back to the navigation mode by selecting the magnifying glass.

  5. Colour in your region that you want to segment by holding down the left mouse button, ensuring that you make a solid object. For 3D structures, set n edit dim to 3 to paint a sphere instead of a circle, or paint circles across several slices. You can change slice using the slider at the bottom of the screen.

A brain region is coloured in

  1. Repeat steps 6.-11. for each other region you would like to segment.

  2. Click Analyse regions to analyse the spatial distribution of the regions you have drawn.

    • If Calculate volumes is selected, the volume of each brain area included in the segmented region will be calculated and saved.

    • If Summarise volumes is selected, then each region will be summarised (centers, volumes etc)

    • If Save segmentation is selected, then the segmented layer will be saved at the same time as the analysis is run (this may make your analysis take longer)

  3. (Optional) Use the Save button to save your segmented regions to be reloaded at a later date.


All data will be saved into your brainreg output directory


For more information about how to use automated methods to segment your feature of interest, please see Analysing segmentation from other napari plugins. For full information on how to use brainglobe-segmentation, please see the brainglobe-segmentation page