Metadata-Version: 2.1
Name: napari-arboretum
Version: 0.1.0
Summary: Track graph and lineage tree visualization with napari
Home-page: https://github.com/quantumjot/arboretum
Author: Alan R. Lowe
Author-email: a.lowe@ucl.ac.uk
License: LICENCE.md
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Framework :: napari
Classifier: Topic :: Software Development :: Testing
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: BSD License
Description-Content-Type: text/markdown
License-File: LICENSE.md

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# Arboretum


![](https://raw.githubusercontent.com/lowe-lab-ucl/arboretum/master/examples/arboretum.gif)
*Automated cell tracking and lineage tree reconstruction*.

### Overview

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

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

---

### 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.



### 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/BayesianTracker/blob/master/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/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
