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Track graph and lineage tree visualization with napari

Project description

License PyPI Python Version tests codecov

Arboretum

Overview

A dockable widget for Napari for visualizing cell lineage trees.

Features:

  • Lineage tree plot widget
  • Integration with btrack

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/stable/napari.layers.Tracks.html#napari.layers.Tracks

To view the legacy version of this plugin, visit the legacy branch:
https://github.com/quantumjot/arboretum/tree/v1-legacy

LineageTree
Automated cell tracking and lineage tree reconstruction.


Installation

We recommend that you first install napari. Detailed instructions are here: https://github.com/napari/napari.

pip install 'napari[all]'

You can install arboretum directly from napari (using the Plugins > Install/Uninstall Packages(s)... menu) and searching for napari-arboretum.

Alternatively, you can install directly from source:

git clone https://github.com/quantumjot/arboretum.git
cd arboretum
pip install -e .

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.

You can use btrack to generate tracks from your image data. See the example notebook here:
https://github.com/quantumjot/BayesianTracker/blob/master/examples/segmentation_to_btrack_to_napari.ipynb


TODO:

  • <input type="checkbox" disabled="" /> Highlight cells in the viewer from the lineage tree view
  • <input type="checkbox" disabled="" /> Visualize merges
  • <input type="checkbox" disabled="" /> Color trees by properties

Project details


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