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).
To load the software, firstly open napari (typically by typing
napari into your command window). You can then
brainreg-segment by navigating to
Add Dock Widget and selecting
The plugin will then open, with some options for loading data:
To load your data#
There are three 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.
Load atlasIf you don’t have your own data registered to the atlas, then you can just load the atlas. Useful for making visualisations etc. Click this drop-down menu, then pick an atlas.