Skip to main content

Track graph and lineage tree visualization with napari

Project description

License PyPI Python Version tests codecov


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:

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

napari-arboretum-0.1.2.tar.gz (9.8 MB view hashes)

Uploaded Source

Built Distribution

napari_arboretum-0.1.2-py3-none-any.whl (18.5 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page