{"id":15690432,"url":"https://github.com/hadim/pytrackmate","last_synced_at":"2025-05-07T23:40:54.736Z","repository":{"id":48979694,"uuid":"131182421","full_name":"hadim/pytrackmate","owner":"hadim","description":"Import Trackmate XML files in Python as Pandas dataframe","archived":false,"fork":false,"pushed_at":"2025-03-01T18:47:12.000Z","size":400,"stargazers_count":9,"open_issues_count":0,"forks_count":6,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-05-07T08:17:16.095Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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/hadim.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.rst","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.rst","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-04-26T16:24:45.000Z","updated_at":"2025-05-03T06:22:57.000Z","dependencies_parsed_at":"2024-10-23T22:59:00.035Z","dependency_job_id":"b1b15cbf-f658-4e10-9ca7-4cd80c179861","html_url":"https://github.com/hadim/pytrackmate","commit_stats":{"total_commits":45,"total_committers":3,"mean_commits":15.0,"dds":0.0444444444444444,"last_synced_commit":"67edb5569a995a73f3539544b8d6c3be670e1926"},"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hadim%2Fpytrackmate","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hadim%2Fpytrackmate/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hadim%2Fpytrackmate/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hadim%2Fpytrackmate/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/hadim","download_url":"https://codeload.github.com/hadim/pytrackmate/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252839354,"owners_count":21812092,"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":"2024-10-03T18:09:24.541Z","updated_at":"2025-05-07T23:40:54.730Z","avatar_url":"https://github.com/hadim.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pytrackmate\n\n[pypi-badge]: https://img.shields.io/pypi/v/pytrackmate\n[release-badge]: https://img.shields.io/github/v/release/hadim/pytrackmate?logo=github\n[test-badge]: https://github.com/hadim/pytrackmate/actions/workflows/test.yaml/badge.svg?branch=main\n[lint-badge]: https://github.com/hadim/pytrackmate/actions/workflows/lint.yaml/badge.svg?branch=main\n\n[![PyPI - Version][pypi-badge]](https://pypi.org/project/pytrackmate/)\n[![GitHub Release][release-badge]](https://github.com/hadim/pytrackmate/releases)\n[![Test CI][test-badge]](https://github.com/hadim/pytrackmate/actions/workflows/test.yaml)\n[![Lint CI][lint-badge]](https://github.com/hadim/pytrackmate/actions/workflows/lint.yaml)\n\nImport [Trackmate](https://imagej.net/TrackMate) XML files in Python as Pandas dataframe.\n\n## Installation 📦\n\n```bash\n# Pip\npip install pytrackmate\n\n# Conda (mamba and micromamba)\nconda install -c conda-forge pytrackmate\n\n# Pixi\npixi add pytrackmate\n```\n\n## Usage 🚀\n\nCheck the [notebook](notebooks/Trackmate.ipynb).\n\n```python\nfname = \"FakeTracks.xml\"\nspots = trackmate_peak_import(fname)\n```\n\n`spots` is a dataframe with the following columns:\n\n- `t_stamp`\n- `t`\n- `x`\n- `y`\n- `z`\n- `w`\n- `q`\n- `spot_id`\n- `mean_intensity`\n- `median_intensity`\n- `min_intensity`\n- `max_intensity`\n- `total_intensity`\n- `std_intensity`\n- `contrast`\n- `snr`\n- `label`\n\n## Development 🛠️\n\nYou need to use [pixi](https://pixi.sh).\n\n```bash\n# Run tests\npixi run -e dev test\n\n# Lint (ruff)\npixi run -e dev lint\n\n# Format code (ruff)\npixi run -e dev format\n```\n\n## Release 🚢\n\nThe package is released on [PyPi](https://pypi.org/project/pytrackmate/) and on conda-forge at \u003chttps://github.com/conda-forge/pytrackmate-feedstock\u003e.\n\nTo cut a new release:\n\n- Trigger [the `release` workflow on the main branch](https://github.com/hadim/pytrackmate/actions/workflows/release.yaml).\n- A new GitHub Release will be created with the new version.\n- The new version will be uploaded on PyPi.\n- The conda-forge bot will create a PR to update the [feedstock](https://github.com/conda-forge/pytrackmate-feedstock).\n- Once the conda-forge PR merged, the new conda version will be available.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhadim%2Fpytrackmate","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhadim%2Fpytrackmate","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhadim%2Fpytrackmate/lists"}