When cellfinder runs, the appropriate machine learning models and reference atlas will be downloaded (if not previously done so). If you would like to download in advance to save time (or if you will not have an internet connection) you can run the following:
To download the machine learning model, run
To download the atlas, please first run
brainglobe list to see the list of available atlases, and then run
brainglobe install -a ATLAS_NAME where
ATLAS_NAME is the atlas you will use for cellfinder (e.g.