About the cellfinder napari plugin
The algorithm that underlies the efficient cell detection in cellfinder is available for use as a plugin for napari. This is a thin wrapper around the cellfinder-core package and aims to:
  • Provide the cell detection algorithm in a user-friendly form
  • Allow the cell detection algorithm to be chained together with other tools in the Napari ecosystem
  • Allow easier parameter optimisation for users of the other cellfinder tools.
Eventually other tools in the BrainGlobe ecosystem (e.g. brainreg) will be developed as napari plugins to provide a full GUI for cell detection, atlas registration and downstream analysis.
Visualising detected cells in the cellfinder napari plugin


First install napari. You can then install the plugin from within napari (Plugins -> Install/Uninstall Package(s), choosing cellfinder-napari).
For analysis of larger images, please also ensure your GPU is set up properly (see Setting up your GPU).


Please see the User guide.