{"id":24432229,"url":"https://github.com/bayer-group/paquo","last_synced_at":"2026-03-10T07:01:33.257Z","repository":{"id":43106902,"uuid":"277534200","full_name":"Bayer-Group/paquo","owner":"Bayer-Group","description":"PAthological QUpath Obsession - QuPath and Python conversations","archived":false,"fork":false,"pushed_at":"2025-08-29T14:28:55.000Z","size":856,"stargazers_count":134,"open_issues_count":32,"forks_count":19,"subscribers_count":8,"default_branch":"main","last_synced_at":"2026-02-24T22:20:12.170Z","etag":null,"topics":["digital-pathology","python","qupath"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Bayer-Group.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":"CODEOWNERS","security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2020-07-06T12:21:16.000Z","updated_at":"2026-02-22T22:39:35.000Z","dependencies_parsed_at":"2024-01-05T23:47:20.734Z","dependency_job_id":"ad06a75c-55d3-4c98-ac9d-d1a285c94b73","html_url":"https://github.com/Bayer-Group/paquo","commit_stats":null,"previous_names":["bayer-science-for-a-better-life/paquo"],"tags_count":19,"template":false,"template_full_name":null,"purl":"pkg:github/Bayer-Group/paquo","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bayer-Group%2Fpaquo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bayer-Group%2Fpaquo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bayer-Group%2Fpaquo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bayer-Group%2Fpaquo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bayer-Group","download_url":"https://codeload.github.com/Bayer-Group/paquo/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bayer-Group%2Fpaquo/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30326893,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-10T05:25:20.737Z","status":"ssl_error","status_checked_at":"2026-03-10T05:25:17.430Z","response_time":106,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["digital-pathology","python","qupath"],"created_at":"2025-01-20T15:36:00.949Z","updated_at":"2026-03-10T07:01:33.247Z","avatar_url":"https://github.com/Bayer-Group.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PAQUO: PAthological QUpath Obsession\n\n[![PyPI Version](https://img.shields.io/pypi/v/paquo)](https://pypi.org/project/paquo/)\n[![Conda (channel only)](https://img.shields.io/conda/vn/conda-forge/paquo?label=conda)](https://anaconda.org/conda-forge/paquo)\n[![Read the Docs](https://img.shields.io/readthedocs/paquo)](https://paquo.readthedocs.io)\n[![paquo ci](https://github.com/bayer-science-for-a-better-life/paquo/actions/workflows/run_pytests.yaml/badge.svg?branch=main)](https://github.com/bayer-science-for-a-better-life/paquo/actions/workflows/run_pytests.yaml)\n[![Codecov](https://img.shields.io/codecov/c/github/bayer-science-for-a-better-life/paquo)](https://codecov.io/gh/bayer-science-for-a-better-life/paquo)\n[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/paquo)](https://github.com/bayer-science-for-a-better-life/paquo)\n[![GitHub issues](https://img.shields.io/github/issues/bayer-science-for-a-better-life/paquo)](https://github.com/bayer-science-for-a-better-life/paquo/issues)\n\nWelcome to `paquo` :wave:, a library for interacting with [QuPath](https://qupath.github.io/)\nfrom [Python](https://www.python.org/).\n\n`paquo`'s goal is to provide a pythonic interface to important features of\nQuPath, and to make creating and working with QuPath projects intuitive for\nPython programmers.\n\nWe strive to make your lives as easy as possible: If `paquo` is not pythonic,\nunintuitive, slow or if its documentation is confusing, it's a bug in\n`paquo`. Feel free to report any issues or feature requests in the issue\ntracker!\n\nDevelopment\n[happens on GitHub](https://github.com/bayer-science-for-a-better-life/paquo)\n:octocat:\n\n## Documentation\n\nYou can find `paquo`'s documentation at\n[paquo.readthedocs.io](https://paquo.readthedocs.io) :heart:\n\n## Installation\n\npaquo's stable releases can be installed via `pip`:\n\n```bash\npip install paquo\n```\n\nor via `conda`:\n\n```bash\nconda install -c conda-forge paquo\n```\n\n## Getting QuPath\n\nAfter installing, paquo requires a QuPath installation to run. To get QuPath follow the\n[installation instructions](https://qupath.readthedocs.io/en/stable/docs/intro/installation.html).\nIf you choose the default installation paths paquo should autodetect your QuPath.\n\nOr you can run the following command to download a specific version of QuPath\nto a location on your machine. Follow the printed instructions to configure\npaquo to use that version. Currently, paquo supports every version of QuPath from\n`0.2.0` to the most recent. We're testing against the newest minor version for\nall supported QuPath releases. _(We even support older `0.2.0-mX` versions but no guarantees)._\n\n```shell\n\u003e paquo get_qupath --install-path \"/some/path/on/your/machine\" 0.6.0\n# downloading: https://github.com/qupath/qupath/releases/download/v0.6.0/QuPath-0.6.0-Linux.tar.xz\n# progress ................... OK\n# extracting: [...]/QuPath-0.6.0-Linux.tar.xz\n# available at: /some/path/on/your/machine/QuPath-0.6.0\n#\n# use via environment variable:\n#   $ export PAQUO_QUPATH_DIR=/some/path/on/your/machine/QuPath-0.6.0\n#\n# use via .paquo.toml config file:\n#   qupath_dir=\"/some/path/on/your/machine/QuPath-0.6.0\"\n/some/path/on/your/machine/QuPath-0.6.0\n```\n\n## Development Installation\n\n1. Install conda and git\n2. Clone paquo `git clone https://github.com/bayer-science-for-a-better-life/paquo.git`\n3. Run `conda env create -f environment.devenv.yml`\n4. Activate the environment `conda activate paquo`\n\nNote that in this environment `paquo` is already installed in development mode,\nso go ahead and hack.\n\n## Contributing Guidelines\n\n- Please follow [pep-8 conventions](https://www.python.org/dev/peps/pep-0008/) but:\n  - We allow 120 character long lines (try anyway to keep them short)\n- Please use [numpy docstrings](https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard).\n- When contributing code, please try to use Pull Requests.\n- tests go hand in hand with modules on `tests` packages at the same level. We use `pytest`.\n\nYou can set up your IDE to help you to adhere to these guidelines.\n\u003cbr\u003e\n_([Santi](https://github.com/sdvillal) is happy to help you to set up pycharm in 5 minutes)_\n\n## Acknowledgements\n\nBuild with love by Andreas Poehlmann and Santi Villalba from the _Machine\nLearning Research_ group at Bayer. In collaboration with the _Pathology Lab 2_\nand the _Mechanistic and Toxicologic Pathology_ group.\n\n`paquo`: copyright 2020 Bayer AG, licensed under [GPL-3.0](https://github.com/bayer-science-for-a-better-life/paquo/blob/master/LICENSE)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbayer-group%2Fpaquo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbayer-group%2Fpaquo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbayer-group%2Fpaquo/lists"}