https://github.com/lowe-lab-ucl/arboretum

Track and lineage visualization with btrack and Napari :evergreen_tree:
https://github.com/lowe-lab-ucl/arboretum

btrack cell-tracking napari visualization

Last synced: 3 months ago
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Track and lineage visualization with btrack and Napari :evergreen_tree:

• Host: GitHub
• URL: https://github.com/lowe-lab-ucl/arboretum
• Owner: lowe-lab-ucl
• License: mit
• Created: 2020-05-13T06:54:51.000Z (about 6 years ago)
• Default Branch: main
• Last Pushed: 2025-09-29T15:14:15.000Z (9 months ago)
• Last Synced: 2025-10-21T19:59:05.218Z (8 months ago)
• Topics: btrack, cell-tracking, napari, visualization
• Language: Python
• Homepage:
• Size: 15.2 MB
• Stars: 46
• Watchers: 5
• Forks: 10
• Open Issues: 15
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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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