Track graph and lineage tree visualization with napari
A dockable widget for Napari for visualizing cell lineage trees.
- 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:
To view the legacy version of this plugin, visit the legacy branch:
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
Alternatively, you can install directly from source:
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 > napari-arboretum menu in napari. To visualize a lineage tree, click on one of the tracks in a napari
You can use btrack to generate tracks from your image data. See the example notebook here:
- Highlight cells in the viewer from the lineage tree view
- Visualize merges
- Color trees by properties
- 14 June 2021
- 11 May 2021
- 4 - Beta
- Stars: 24
- Forks: 4
- Issues + PRs: 3
Python versions supported:
- OS Independent
- numpy (>=1.17.3)
- scipy (>=1.3.1)
- napari (>=0.4.0)
- pyqtgraph (>=0.10.0)