{"id":29227227,"url":"https://github.com/royerlab/trackedit","last_synced_at":"2025-07-03T09:10:17.585Z","repository":{"id":281933823,"uuid":"930639735","full_name":"royerlab/trackedit","owner":"royerlab","description":"Interactive tracks editing tool for Ultrack","archived":false,"fork":false,"pushed_at":"2025-06-03T21:04:39.000Z","size":419,"stargazers_count":4,"open_issues_count":13,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-06-04T03:16:57.023Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/royerlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","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":"2025-02-11T00:48:14.000Z","updated_at":"2025-06-03T20:54:50.000Z","dependencies_parsed_at":"2025-03-11T23:26:55.601Z","dependency_job_id":"c9e790fb-5edb-4828-b0b7-b454f9d65548","html_url":"https://github.com/royerlab/trackedit","commit_stats":null,"previous_names":["royerlab/trackedit"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/royerlab/trackedit","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/royerlab%2Ftrackedit","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/royerlab%2Ftrackedit/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/royerlab%2Ftrackedit/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/royerlab%2Ftrackedit/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/royerlab","download_url":"https://codeload.github.com/royerlab/trackedit/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/royerlab%2Ftrackedit/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263296638,"owners_count":23444499,"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","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":[],"created_at":"2025-07-03T09:10:15.778Z","updated_at":"2025-07-03T09:10:17.557Z","avatar_url":"https://github.com/royerlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003c!-- [![PyPI - Version](https://img.shields.io/pypi/v/trackedit.svg)](https://pypi.org/project/trackedit) --\u003e\n\u003c!-- [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/trackedit.svg)](https://pypi.org/project/trackedit) --\u003e\n[![Tests](https://github.com/royerlab/trackedit/actions/workflows/tests.yml/badge.svg)](https://github.com/royerlab/trackedit/actions/workflows/tests.yml)\n[![codecov](https://codecov.io/gh/royerlab/trackedit/branch/main/graph/badge.svg)](https://codecov.io/gh/royerlab/trackedit)\n\n# TrackEdit ⛓️\n\nSet of napari widget to interactively proofread, edit, and annotate, cell tracking data tracked with [Ultrack](https://github.com/royerlab/ultrack).\n\n-----\n\n`TrackEdit` napari UI:\n\n\u003cimg width=\"1449\" alt=\"UI2\" src=\"https://github.com/user-attachments/assets/c9d0c209-cb87-4820-af68-1744ef4dcb90\" /\u003e\n\n## Installation HPC 🖥️\n\n1. Clone repo in $MYDATA and install pixi environment\n```console\ngit clone https://github.com/royerlab/trackedit.git --recurse-submodules\ncd trackedit\nmodule load pixi\npixi install\npixi shell\n```\n\nAlternatively, you can activate the environment using conda `conda activate .pixi/envs/default` (after `pixi install`)\n\n2. `cd` to relevant data folder (that contains `data.db` and `metadata.toml`), copy `scripts/demo.py` script, change relevant input parameters, and run inTRACKtive:\n```\npython demo_neuromast.py #_after changing relevant parameters\n```\nNote: make sure to first `pixi shell` in the $MYDATA directory, before running the python script. This is the equivalent of `conda activate ...`\n\n### Keyboard shortcuts ⌨️\n\n#### Napari Viewer and Layer Controls\n| Mouse / Key binding | Action |\n|-------------------|---------|\n| Click on point/label | Select node (centers view if needed) |\n| SHIFT + click | Add node to selection |\n| Q | Toggle between all nodes view and selected lineages only |\n\n#### Tree View Controls\n| Mouse / Key binding | Action |\n|-------------------|---------|\n| Click on node | Select node (centers view if needed) |\n| SHIFT + click | Add node to selection |\n| Scroll | Zoom in/out |\n| Scroll + X / Right click + drag horizontally | Zoom x-axis only |\n| Scroll + Y / Right click + drag vertically | Zoom y-axis only |\n| Mouse drag | Pan |\n| SHIFT + Mouse drag | Rectangular node selection |\n| Right click | Reset view |\n| Q | Toggle between all lineages (vertical) and selected lineages (horizontal) |\n| ~~W~~ | ~~Switch between lineage tree and object size plot~~ |\n| ← | Select node to the left |\n| → | Select node to the right |\n| ↑ | Select parent node (vertical) or next lineage (horizontal) |\n| ↓ | Select child node (vertical) or previous lineage (horizontal) |\n\n#### Track Editing\n| Mouse / Key binding | Action |\n|-------------------|---------|\n| D | Delete selected nodes |\n| B | Break edge between selected nodes |\n| A | Create edge between selected nodes (if valid) |\n| Z | Undo last edit |\n| R | Redo last edit |\n\n## Credits 🙌\nThe `TrackEdit` widget structure is inspired by, and built upon, [Motile_tracker](https://github.com/funkelab/motile_tracker) (Funke lab, HHMI Janelia Research Campus)\n\n## License 🔓\n\n`trackedit` is distributed under the terms of the [MIT](https://spdx.org/licenses/MIT.html) license.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Froyerlab%2Ftrackedit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Froyerlab%2Ftrackedit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Froyerlab%2Ftrackedit/lists"}