Track graph and lineage tree visualization with napari
Project description
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.
: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
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
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.
Project details
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