{"id":28693214,"url":"https://github.com/cytomining/cytodataframe","last_synced_at":"2025-06-14T08:11:12.457Z","repository":{"id":260350808,"uuid":"876994333","full_name":"cytomining/CytoDataFrame","owner":"cytomining","description":"An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.","archived":false,"fork":false,"pushed_at":"2025-06-11T16:50:05.000Z","size":72657,"stargazers_count":2,"open_issues_count":16,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-06-11T18:12:10.604Z","etag":null,"topics":["dataframes","image-analysis","image-based-profiling","single-cell"],"latest_commit_sha":null,"homepage":"https://cytomining.github.io/CytoDataFrame","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cytomining.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2024-10-22T22:47:10.000Z","updated_at":"2025-06-11T16:49:21.000Z","dependencies_parsed_at":"2025-01-20T15:21:34.891Z","dependency_job_id":"bdad180e-f5ae-4d60-9a9a-1da88af3ae5b","html_url":"https://github.com/cytomining/CytoDataFrame","commit_stats":null,"previous_names":["wayscience/cytodataframe","cytomining/cytodataframe"],"tags_count":14,"template":false,"template_full_name":null,"purl":"pkg:github/cytomining/CytoDataFrame","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cytomining%2FCytoDataFrame","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cytomining%2FCytoDataFrame/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cytomining%2FCytoDataFrame/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cytomining%2FCytoDataFrame/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cytomining","download_url":"https://codeload.github.com/cytomining/CytoDataFrame/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cytomining%2FCytoDataFrame/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259783067,"owners_count":22910301,"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":["dataframes","image-analysis","image-based-profiling","single-cell"],"created_at":"2025-06-14T08:11:11.416Z","updated_at":"2025-06-14T08:11:12.449Z","avatar_url":"https://github.com/cytomining.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CytoDataFrame\n\n[![PyPI - Version](https://img.shields.io/pypi/v/cytodataframe)](https://pypi.org/project/CytoDataFrame/)\n[![Build Status](https://github.com/cytomining/CytoDataFrame/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/cytomining/CytoDataFrame/actions/workflows/run-tests.yml?query=branch%3Amain)\n![Coverage Status](https://raw.githubusercontent.com/cytomining/CytoDataFrame/main/media/coverage-badge.svg)\n[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)\n[![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)\n[![Software DOI badge](https://zenodo.org/badge/DOI/10.5281/zenodo.14797074.svg)](https://doi.org/10.5281/zenodo.14797074)\n\n![](https://raw.githubusercontent.com/cytomining/coSMicQC/refs/heads/main/docs/presentations/2024-09-18-SBI2-Conference/images/cosmicqc-example-cytodataframe.png)\n_CytoDataFrame extends Pandas functionality to help display single-cell profile data alongside related images._\n\nCytoDataFrame is an advanced in-memory data analysis format designed for single-cell profiling, integrating not only the data profiles but also their corresponding microscopy images and segmentation masks.\nTraditional single-cell profiling often excludes the associated images from analysis, limiting the scope of research.\nCytoDataFrame bridges this gap, offering a purpose-built solution for comprehensive analysis that incorporates both the data and images, empowering more detailed and visual insights in single-cell research.\n\nCytoDataFrame is best suited for work within Jupyter notebooks.\nWith CytoDataFrame you can:\n\n- View image objects alongside their feature data using a Pandas DataFrame-like interface.\n- Highlight image objects using mask or outline files to understand their segmentation.\n- Adjust image displays on-the-fly using interactive slider widgets.\n\n📓 ___Want to see CytoDataFrame in action?___ Check out our [example notebook](docs/src/examples/cytodataframe_at_a_glance.ipynb) for a quick tour of its key features.\n\n\u003e ✨ CytoDataFrame development began within **[coSMicQC](https://github.com/cytomining/coSMicQC)** - a single-cell profile quality control package.\n\u003e Please check out our work there as well!\n\n## Installation\n\nInstall CytoDataFrame from source using the following:\n\n```shell\n# install from pypi\npip install cytodataframe\n\n# or install directly from source\npip install git+https://github.com/cytomining/CytoDataFrame.git\n```\n\n## Contributing, Development, and Testing\n\nPlease see our [contributing](https://cytomining.github.io/CytoDataFrame/main/contributing) documentation for more details on contributions, development, and testing.\n\n## References\n\n- [coSMicQC](https://github.com/cytomining/coSMicQC)\n- [pycytominer](https://github.com/cytomining/pycytominer)\n- [CellProfiler](https://github.com/CellProfiler/CellProfiler)\n- [CytoTable](https://github.com/cytomining/CytoTable)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcytomining%2Fcytodataframe","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcytomining%2Fcytodataframe","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcytomining%2Fcytodataframe/lists"}