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Track graph and lineage tree visualization with napari

Project description

License PyPI Python Version tests codecov



A dockable widget for Napari for visualizing cell lineage trees.


  • Lineage tree plot widget
  • Integration with btrack

This project has changed considerably. The Tracks layer, originally developed for this plugin, is now an official layer type in napari. Read the napari documentation here:

To view the legacy version of this plugin, visit the legacy branch:

Automated cell tracking and lineage tree reconstruction.


We recommend that you first install napari. Detailed instructions are here:

pip install 'napari[all]'

You can install arboretum directly from napari (using the Plugins > Install/Uninstall Packages(s)... menu) and searching for napari-arboretum.

Alternatively, you can install directly from source:

git clone
cd arboretum
pip install -e .


Once installed, Arboretum will be visible in the Plugins > Add Dock Widget > napari-arboretum menu in napari. To visualize a lineage tree, click on one of the tracks in a napari Tracks layer.

You can use btrack to generate tracks from your image data. See the example notebook here:


  • <input type="checkbox" disabled="" /> Highlight cells in the viewer from the lineage tree view
  • <input type="checkbox" disabled="" /> Visualize merges
  • <input type="checkbox" disabled="" /> Color trees by properties

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