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Arboretum

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Automated cell tracking and lineage tree reconstruction.

Overview

A dockable widget for Napari for visualizing cell lineage trees.

Features:

  • Lineage tree plot widget
  • Integration with btrack

Usage

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.

Examples

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.py

Alternatively, you can use btrack to generate tracks from your image data. See the example notebook here: https://github.com/quantumjot/btrack/blob/main/examples

History

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