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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.
{% hint style="info" %} 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. {% endhint %}
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.