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Automated cell tracking and lineage tree reconstruction.
A dockable widget for Napari for visualizing cell lineage trees.
Features:
- 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/show_sample_data.pyAlternatively, you can use btrack to generate tracks from your image data. See the example notebook here: https://github.com/quantumjot/btrack/blob/main/examples
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:
https://napari.org/stable/api/napari.layers.Tracks.html
To view the legacy version of this plugin, visit the legacy branch: https://github.com/quantumjot/arboretum/tree/v1-legacy