Prerequisites#

Your data must have been registered to an atlas using brainreg (or the brainreg-based registration within cellfinder).

Please follow the instructions for these packages, and ensure that the channel that you want to segment is downsampled (e.g., using the --downsample flag in brainreg).

Usage#

To load the software, firstly open napari (typically by typing napari into your command window). You can then load brainglobe-segmentation by navigating to Plugins -> Add Dock Widget and selecting brainglobe-segmentation.

The plugin will then open, with some options for loading data:

brainreg interface

To load your data#

There are two options for loading your data (in the Load data section of the GUI):

  • Load project (sample space) - This is for loading a brainreg project in the coordinate space of your raw data (i.e., not warped to the atlas space). N.B. the data will have been reoriented to the orientation of your chosen atlas, but it can be reoriented using the napari button in the bottom left (a cube with an arrow above it). Click this button, then choose your brainreg (or cellfinder registration) output directory.

  • Load project (atlas space) - As above, but the data loaded will have been warped into the atlas space. This is most useful when you want to visualise your segmented structures in brainrender, as they must be in atlas space to do so. Click this button, then choose your brainreg (or cellfinder registration) output directory.