napari-arboretum 0.0.1

Track graph and lineage tree visualization with napari

Arboretum

Overview

A dockable widget for Napari for visualizing cell lineage trees.

Features:

• Lineage tree plot widget
• Integration with btrack

Automated cell tracking and lineage tree reconstruction.

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:construction: WORK IN PROGRESS :construction:

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

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TODO:

• Refactor for Napari 0.4.0 (now including napari.layers.Tracks!)
• Highlight cells in the viewer from the lineage tree view
• Visualize merges
• Color trees by properties

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Installation

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

pip install napari[all]

then install arboretum:

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

Once installed, Arboretum will be visible in the Plugins > Add Dock Widget > arboretum menu in napari.