napari-arboretum

Track graph and lineage tree visualization with napari


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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, 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/BayesianTracker/blob/master/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/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

Version:

  • 0.1.0

Release date:

  • 10 June 2022

First released:

  • 11 May 2021

License:

  • MIT

Supported data:

  • Information not submitted

GitHub activity:

  • Stars: 32
  • Forks: 8
  • Issues + PRs: 20

Python versions supported:

Operating system:

Requirements:

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

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