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
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
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:
- Highlight cells in the viewer from the lineage tree view
- Visualize merges
- Color trees by properties
Project details
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