Version:

  • 0.0.2

Release date:

  • 14 June 2021

First released:

  • 11 May 2021

License:

  • MIT

GitHub activity:

  • Stars: 24
  • Forks: 4
  • Issues + PRs: 3

Python versions supported:

  • >=3.6

Operating system:

  • OS Independent

Requirements:

  • numpy (>=1.17.3)
  • scipy (>=1.3.1)
  • napari (>=0.4.0)
  • pyqtgraph (>=0.10.0)

    napari-arboretum

    Track graph and lineage tree visualization with napari

    Authors:

    • Alan R. Lowe

    Learn more:

    Source code:

    Authors:

    • Alan R. Lowe

    Learn more:

    Source code:

    License PyPI Python Version tests codecov

    Overview

    A dockable widget for Napari for visualizing cell lineage trees.

    Features:

    • 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:
    https://napari.org/api/stable/napari.layers.Tracks.html#napari.layers.Tracks

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

    LineageTree
    Automated cell tracking and lineage tree reconstruction.


    Installation

    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 napari-arboretum.

    Alternatively, you can install directly from source:

    git clone https://github.com/quantumjot/arboretum.git
    cd arboretum
    pip install -e .

    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.

    You can use btrack to generate tracks from your image data. See the example notebook here:
    https://github.com/quantumjot/BayesianTracker/blob/master/examples/segmentation_to_btrack_to_napari.ipynb


    TODO:

    • Highlight cells in the viewer from the lineage tree view
    • Visualize merges
    • Color trees by properties

    Version:

    • 0.0.2

    Release date:

    • 14 June 2021

    First released:

    • 11 May 2021

    License:

    • MIT

    GitHub activity:

    • Stars: 24
    • Forks: 4
    • Issues + PRs: 3

    Python versions supported:

    • >=3.6

    Operating system:

    • OS Independent

    Requirements:

    • numpy (>=1.17.3)
    • scipy (>=1.3.1)
    • napari (>=0.4.0)
    • pyqtgraph (>=0.10.0)

    Version:

    • 0.0.2

    Release date:

    • 14 June 2021

    First released:

    • 11 May 2021

    License:

    • MIT

    GitHub activity:

    • Stars: 24
    • Forks: 4
    • Issues + PRs: 3

    Python versions supported:

    • >=3.6

    Operating system:

    • OS Independent

    Requirements:

    • numpy (>=1.17.3)
    • scipy (>=1.3.1)
    • napari (>=0.4.0)
    • pyqtgraph (>=0.10.0)

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