Segmenting 2/3D structures#

To segment a 3D (or 2D) structure, such as an injection site, select the Region Segmentation button in the Segmentation panel.

Segmenting a 2/3D structure


  • Click the Add region buttons

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

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

  • Choose a brush size (top left box). N.B. this is in 3D.

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

  • mode by selecting the magnifying glass.

  • Colour in your region that you want to segment, ensuring that you make a

    solid object.

  • Add a new region if required (Add region)

  • Repeat above for each region you wish to segment.

  • 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)

You can also use Save independently of the analysis to save your regions to be reloaded at a later date, and if you loaded your data in atlas space, you can also export the regions to brainrender.


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.