Downloading files

Downloading the files that cellfinder needs

Download atlas and trained classification models (optional)
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 cellfinder_download
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. allen_mouse_25um).

Installation with SLURM

Setting up your GPU