{"id":32176375,"url":"https://github.com/lowe-lab-ucl/arboretum","last_synced_at":"2026-03-11T03:01:59.397Z","repository":{"id":38105728,"uuid":"263549750","full_name":"lowe-lab-ucl/arboretum","owner":"lowe-lab-ucl","description":"Track and lineage visualization with btrack and Napari :evergreen_tree:","archived":false,"fork":false,"pushed_at":"2025-09-29T15:14:15.000Z","size":15973,"stargazers_count":46,"open_issues_count":15,"forks_count":10,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-10-21T19:59:05.218Z","etag":null,"topics":["btrack","cell-tracking","napari","visualization"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lowe-lab-ucl.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2020-05-13T06:54:51.000Z","updated_at":"2025-10-03T05:55:29.000Z","dependencies_parsed_at":"2025-08-22T22:16:59.709Z","dependency_job_id":"ef2f4ba6-2bf3-4027-8709-5ee27aada58d","html_url":"https://github.com/lowe-lab-ucl/arboretum","commit_stats":null,"previous_names":["quantumjot/arboretum"],"tags_count":8,"template":false,"template_full_name":null,"purl":"pkg:github/lowe-lab-ucl/arboretum","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lowe-lab-ucl%2Farboretum","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lowe-lab-ucl%2Farboretum/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lowe-lab-ucl%2Farboretum/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lowe-lab-ucl%2Farboretum/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lowe-lab-ucl","download_url":"https://codeload.github.com/lowe-lab-ucl/arboretum/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lowe-lab-ucl%2Farboretum/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280325297,"owners_count":26311419,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-21T02:00:06.614Z","response_time":58,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["btrack","cell-tracking","napari","visualization"],"created_at":"2025-10-21T19:59:13.258Z","updated_at":"2025-10-21T19:59:14.864Z","avatar_url":"https://github.com/lowe-lab-ucl.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Downloads](https://pepy.tech/badge/napari-arboretum)](https://pepy.tech/project/napari-arboretum)\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 \u003e Add Dock Widget \u003e 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","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flowe-lab-ucl%2Farboretum","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flowe-lab-ucl%2Farboretum","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flowe-lab-ucl%2Farboretum/lists"}