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) please use cellfinder_download.

Currently, the only supported atlas is the Allen reference mouse brain, originally from here. The atlas will download into ./cellfinder/atlas.

In the future, other atlases will be available, and you will be able to choose which is downloaded.

If you want to modify the cellfinder download, use:

  • --atlas-install-path Supply a path to download the atlas elsewhere. This

    should also update the default cellfinder.conf file so that the correct

    atlas is sourced. Alternatively, use this command to tell cellfinder where an

    existing atlas is, to save it being downloaded twice. (Requires 20GB

    disk space)

  • --atlas download path The path to download the atlas into.

    (Requires 1.2GB disk space). Defaults to /tmp.

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