BrainGlobe version 1 is here! Head over to the blog to find out more

Downloading the pre-trained model in advance#

cellfinder will download the pre-trained model when it’s needed. However, you may want to download this model in advance to save time later, or if you know your internet connection will be disrupted. For this reason, cellfinder comes with a command-line tool (cellfinder_download) to download a pre-trained model.

To download the recommended model, just run cellfinder_download. However, you can also use the following options:

  • --install-path Use this flag to choose where you would like to download the model to, and also update the cellfinder config file (at ~/.brainglobe/cellfinder/cellfinder.conf.custom) to point to this location. By default, models are saved in your home directory at ~/.brainglobe/cellfinder/models.

  • --model Use this flag to specify a specific model. The default model is restnet50_tv, which is (currently) the only recommended model to use.

  • --no-amend-config Use this flag to ensure the cellfinder config file is not updated (useful if you just want to download the trained model)