Track graph and lineage tree visualization with napari

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    Automated cell tracking and lineage tree reconstruction.


    A dockable widget for Napari for visualizing cell lineage trees.


    • Lineage tree plot widget
    • Integration with btrack


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


    You can use the example script to display some sample tracking data in napari and load the arboretum tree viewer:

    python ./examples/

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


    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:


    • 0.1.2

    Last updated:

    • 07 June 2023

    First released:

    • 11 May 2021


    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

    • Stars: 42
    • Forks: 11
    • Issues + PRs: 14

    Python versions supported:

    Operating system:


    • matplotlib
    • napari-matplotlib (>=0.2.1)
    • napari (>=0.4.0)
    • numpy (>=1.17.3)
    • pandas
    • pooch (>=1)
    • qtpy
    • scikit-image
    • vispy

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