Track graph and lineage tree visualization with napari

Workflow step:
Object trackingIsolated object trackingCell tracking
Object trackingCell lineage extraction
Object tracking

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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:


  • 0.1.1

Last updated:

  • 13 September 2022

First released:

  • 11 May 2021


  • MIT

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 38
  • Forks: 10
  • Issues + PRs: 16

Python versions supported:

Operating system:


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

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