{"name":"napari-arboretum","display_name":"napari-arboretum","visibility":"public","icon":"","categories":[],"schema_version":"0.1.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-arboretum.Arboretum","title":"Create Arboretum","python_name":"napari_arboretum._hookimpls:Arboretum","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-arboretum.Arboretum","display_name":"Arboretum","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-arboretum","version":"0.1.2","dynamic":null,"platform":null,"supported_platform":null,"summary":"Track graph and lineage tree visualization with napari","description":" <!--[![Downloads](https://pepy.tech/badge/napari-arboretum)](https://pepy.tech/project/napari-arboretum)-->\n\n[![License](https://img.shields.io/pypi/l/napari-arboretum.svg?color=green)](https://github.com/lowe-lab-ucl/arboretum/blob/main/LICENSE.md)\n[![PyPI](https://img.shields.io/pypi/v/napari-arboretum.svg?color=green)](https://pypi.org/project/napari-arboretum)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-arboretum.svg?color=green)](https://python.org)\n[![tests](https://github.com/lowe-lab-ucl/arboretum/workflows/tests/badge.svg)](https://github.com/lowe-lab-ucl/arboretum/actions)\n[![codecov](https://codecov.io/gh/lowe-lab-ucl/arboretum/branch/main/graph/badge.svg?token=2M2HhM60op)](https://app.codecov.io/gh/lowe-lab-ucl/arboretum/tree/main)\n\n# Arboretum\n\n\n\nhttps://github.com/lowe-lab-ucl/arboretum/assets/8217795/d98c22c4-73bb-493a-9f8f-c224d615209d\n\n\n_Automated cell tracking and lineage tree reconstruction_.\n\n### Overview\n\nA dockable widget for [Napari](https://github.com/napari/napari) for visualizing cell lineage trees.\n\nFeatures:\n\n- Lineage tree plot widget\n- Integration with [btrack](https://github.com/quantumjot/btrack)\n\n---\n\n### Usage\n\nOnce 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.\n\n### Examples\n\nYou can use the example script to display some sample tracking data in napari and load the arboretum tree viewer:\n\n```sh\npython ./examples/show_sample_data.py\n```\n\nAlternatively, you can use _btrack_ to generate tracks from your image data. See the example notebook here:\nhttps://github.com/quantumjot/btrack/blob/main/examples\n\n---\n\n### History\n\nThis 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:\nhttps://napari.org/stable/api/napari.layers.Tracks.html\n\nTo view the legacy version of this plugin, visit the legacy branch:\nhttps://github.com/quantumjot/arboretum/tree/v1-legacy\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"\"Alan R. Lowe\" <a.lowe@ucl.ac.uk>","maintainer":null,"maintainer_email":null,"license":null,"classifier":["Development Status :: 4 - Beta","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python :: 3","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Programming Language :: Python","Topic :: Scientific/Engineering :: Visualization"],"requires_dist":["matplotlib","napari-matplotlib (>=0.2.1)","napari (>=0.4.0)","numpy (>=1.17.3)","pandas","pooch (>=1)","qtpy","scikit-image","vispy"],"requires_python":">=3.8","requires_external":null,"project_url":["homepage, https://github.com/lowe-lab-ucl/arboretum"],"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}