{"id":20874436,"url":"https://github.com/imagingdatacommons/idc-index","last_synced_at":"2026-01-24T00:44:55.016Z","repository":{"id":206550319,"uuid":"716718400","full_name":"ImagingDataCommons/idc-index","owner":"ImagingDataCommons","description":"Python package to simplify access to the data available from NCI Imaging Data Commons","archived":false,"fork":false,"pushed_at":"2024-11-13T21:45:10.000Z","size":946,"stargazers_count":11,"open_issues_count":17,"forks_count":5,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-11-13T22:29:41.031Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://idc-index.readthedocs.io/","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/ImagingDataCommons.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":".github/CONTRIBUTING.md","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":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-11-09T18:15:13.000Z","updated_at":"2024-11-13T21:45:15.000Z","dependencies_parsed_at":"2023-11-27T05:23:43.679Z","dependency_job_id":"68267dc8-7308-4fb3-b741-67946c706176","html_url":"https://github.com/ImagingDataCommons/idc-index","commit_stats":null,"previous_names":["vkt1414/idc_index","imagingdatacommons/idc-index"],"tags_count":38,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImagingDataCommons%2Fidc-index","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImagingDataCommons%2Fidc-index/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImagingDataCommons%2Fidc-index/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImagingDataCommons%2Fidc-index/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ImagingDataCommons","download_url":"https://codeload.github.com/ImagingDataCommons/idc-index/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225139245,"owners_count":17426944,"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":"2024-11-18T06:32:29.065Z","updated_at":"2026-01-24T00:44:54.960Z","avatar_url":"https://github.com/ImagingDataCommons.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# idc-index\n\n[![Actions Status][actions-badge]][actions-link]\n[![Documentation Status][rtd-badge]][rtd-link]\n\n[![PyPI version][pypi-version]][pypi-link]\n[![PyPI platforms][pypi-platforms]][pypi-link]\n\n[![Discourse Forum][discourse-forum-badge]][discourse-forum-link]\n\n\u003e [!WARNING]\n\u003e\n\u003e This package is in its early development stages. Its functionality and API\n\u003e will change.\n\u003e\n\u003e Stay tuned for the updates and documentation, and please share your feedback\n\u003e about it by opening issues in this repository, or by starting a discussion in\n\u003e [IDC User forum](https://discourse.canceridc.dev/).\n\n\u003c!-- SPHINX-START --\u003e\n\n## About\n\n`idc-index` is a Python package that enables basic operations for working with\n[NCI Imaging Data Commons (IDC)](https://imaging.datacommons.cancer.gov):\n\n- subsetting of the IDC data using selected metadata attributes\n- download of the files corresponding to selection\n- generation of the viewer URLs for the selected data\n\n## Getting started\n\nInstall the latest version of the package.\n\n```bash\n$ pip install --upgrade idc-index\n```\n\nInstantiate `IDCClient`, which provides the interface for main operations.\n\n```python\nfrom idc_index import IDCClient\n\nclient = IDCClient.client()\n```\n\nYou can use [IDC Portal](https://imaging.datacommons.cancer.gov/explore/) to\nbrowse collections, cases, studies and series, copy their identifiers and\ndownload the corresponding files using `idc-index` helper functions.\n\nYou can try this out with the `rider_pilot` collection, which is just 10.5 GB in\nsize:\n\n```\nclient.download_from_selection(collection_id=\"rider_pilot\", downloadDir=\".\")\n```\n\n... or run queries against the \"mini\" index of Imaging Data Commons data, and\ndownload images that match your selection criteria! The following will select\nall Magnetic Resonance (MR) series, and will download the first 10.\n\n```python\nfrom idc_index import index\n\nclient = index.IDCClient()\n\nquery = \"\"\"\nSELECT\n  SeriesInstanceUID\nFROM\n  index\nWHERE\n  Modality = 'MR'\n\"\"\"\n\nselection_df = client.sql_query(query)\n\nclient.download_from_selection(\n    seriesInstanceUID=list(selection_df[\"SeriesInstanceUID\"].values[:10]),\n    downloadDir=\".\",\n)\n```\n\n## Tutorial\n\nPlease check out\n[this tutorial notebook](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/labs/idc_rsna2023.ipynb)\nfor the introduction into using `idc-index`.\n\n## Resources\n\n- [Imaging Data Commons Portal](https://imaging.datacommons.cancer.gov/) can be\n  used to explore the content of IDC from the web browser\n- [s5cmd](https://github.com/peak/s5cmd) is a highly efficient, open source,\n  multi-platform S3 client that we use for downloading IDC data, which is hosted\n  in public AWS and GCS buckets. Distributed on PyPI as\n  [s5cmd](https://pypi.org/project/s5cmd/).\n- [SlicerIDCBrowser](https://github.com/ImagingDataCommons/SlicerIDCBrowser) 3D\n  Slicer extension that relies on `idc-index` for search and download of IDC\n  data\n\n## Acknowledgment\n\nThis software is maintained by the IDC team, which has been funded in whole or\nin part with Federal funds from the NCI, NIH, under task order no. HHSN26110071\nunder contract no. HHSN261201500003l.\n\nIf this package helped your research, we would appreciate if you could cite IDC\npaper below.\n\n\u003e Fedorov, A., Longabaugh, W. J. R., Pot, D., Clunie, D. A., Pieper, S. D.,\n\u003e Gibbs, D. L., Bridge, C., Herrmann, M. D., Homeyer, A., Lewis, R., Aerts, H.\n\u003e J. W., Krishnaswamy, D., Thiriveedhi, V. K., Ciausu, C., Schacherer, D. P.,\n\u003e Bontempi, D., Pihl, T., Wagner, U., Farahani, K., Kim, E. \u0026 Kikinis, R.\n\u003e _National Cancer Institute Imaging Data Commons: Toward Transparency,\n\u003e Reproducibility, and Scalability in Imaging Artificial Intelligence_.\n\u003e RadioGraphics (2023). https://doi.org/10.1148/rg.230180\n\n\u003c!-- prettier-ignore-start --\u003e\n[actions-badge]:            https://github.com/ImagingDataCommons/idc-index/workflows/CI/badge.svg\n[actions-link]:             https://github.com/ImagingDataCommons/idc-index/actions\n[discourse-forum-badge]: https://img.shields.io/discourse/https/discourse.canceridc.dev/status.svg\n[discourse-forum-link]:  https://discourse.canceridc.dev/\n[pypi-link]:                https://pypi.org/project/idc-index/\n[pypi-platforms]:           https://img.shields.io/pypi/pyversions/idc-index\n[pypi-version]:             https://img.shields.io/pypi/v/idc-index\n[rtd-badge]:                https://readthedocs.org/projects/idc-index/badge/?version=latest\n[rtd-link]:                 https://idc-index.readthedocs.io/en/latest/?badge=latest\n\n\u003c!-- prettier-ignore-end --\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fimagingdatacommons%2Fidc-index","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fimagingdatacommons%2Fidc-index","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fimagingdatacommons%2Fidc-index/lists"}