semvec/pypi-packages huggingface dataset:
napari-arboretum 0.2.0
Track graph and lineage tree visualization with napari
Requires Python: >=3.10

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# Arboretum



https://github.com/lowe-lab-ucl/arboretum/assets/8217795/d98c22c4-73bb-493a-9f8f-c224d615209d


_Automated cell tracking and lineage tree reconstruction_.

### Overview

A dockable widget for [Napari](https://github.com/napari/napari) for visualizing cell lineage trees.

Features:

- Lineage tree plot widget
- Integration with [btrack](https://github.com/quantumjot/btrack)

---

### Usage

Once installed, Arboretum will be visible in the `Plugins > Add Dock Widget > napari-arboretum` menu in napari. To visualize a lineage tree, (double) click on one of the tracks in a napari `Tracks` layer.

### Examples

You can use the example script to display some sample tracking data in napari and load the arboretum tree viewer:

```sh
python ./examples/show_sample_data.py
```

Alternatively, you can use _btrack_ to generate tracks from your image data. See the example notebook here:
https://github.com/quantumjot/btrack/blob/main/examples

---

### History

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/stable/api/napari.layers.Tracks.html

To view the legacy version of this plugin, visit the legacy branch:
https://github.com/quantumjot/arboretum/tree/v1-legacy