napari-relax

ReLAX (Reconstructed Lineage Analysis & eXploration) is a napari plugin to visualise and compare cell lineage trees. It gives LineageTree datasets a graphical interface, so no programming is needed.

Documentation: guignardlab.github.io/napari-relax

Features

• Explore tracking datasets in the napari viewer and in an interactive Lineage Viewer, side by side.
• Relabel lineages and save them as .lT files.
• Recolor cells by clone or by any numeric attribute of the dataset.
• Compare lineages and sublineages with unordered tree edit distances, shown as an interactive clustermap.
• Compare across datasets, even with different time resolutions.

ReLAX opens .lT, MaMuT and ASTEC .xml, Mastodon and .bmf files, and comes with two demo datasets under File > Open Sample > ReLAX.

Installation

ReLAX requires Python 3.10 or newer and napari 0.9 or newer. You can install napari-relax via pip:

pip install napari-relax

If napari is not already installed, you can install napari-relax with napari and Qt via:

pip install "napari-relax[all]"

To install the latest development version:

pip install git+https://github.com/guignardlab/napari-relax.git

Then open Plugins > Lineage tree analysis or Plugins > Cross Lineagetree comparison in napari. The Quick Start walks through a first session.

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

The documentation is built with MkDocs from the docs/ folder and published automatically when main changes. To preview it locally:

pip install -e ".[docs]"
mkdocs serve

See the developer documentation for an overview of the code.

License

Distributed under the terms of the BSD-3 license, "napari-relax" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

This napari plugin was generated with copier using the napari-plugin-template.