{"id":13752239,"url":"https://github.com/ome/ome-zarr-py","last_synced_at":"2026-04-14T11:01:22.334Z","repository":{"id":36960993,"uuid":"261714880","full_name":"ome/ome-zarr-py","owner":"ome","description":"Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.","archived":false,"fork":false,"pushed_at":"2026-04-14T09:43:07.000Z","size":1779,"stargazers_count":230,"open_issues_count":77,"forks_count":66,"subscribers_count":16,"default_branch":"master","last_synced_at":"2026-04-14T10:26:28.897Z","etag":null,"topics":["ngff","ome","ome-zarr","zarr"],"latest_commit_sha":null,"homepage":"https://ome-zarr.readthedocs.io/en/stable/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ome.png","metadata":{"files":{"readme":"README.rst","changelog":"CHANGELOG.md","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":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2020-05-06T09:40:59.000Z","updated_at":"2026-04-14T09:30:26.000Z","dependencies_parsed_at":"2023-11-09T02:03:12.778Z","dependency_job_id":"e4dd6ae1-39c8-4b25-ba2e-92ab8e9f6376","html_url":"https://github.com/ome/ome-zarr-py","commit_stats":{"total_commits":856,"total_committers":38,"mean_commits":"22.526315789473685","dds":0.7429906542056075,"last_synced_commit":"56f72b06d4912ba5156fe54f913d19df895b9e9e"},"previous_names":[],"tags_count":60,"template":false,"template_full_name":null,"purl":"pkg:github/ome/ome-zarr-py","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ome%2Fome-zarr-py","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ome%2Fome-zarr-py/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ome%2Fome-zarr-py/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ome%2Fome-zarr-py/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ome","download_url":"https://codeload.github.com/ome/ome-zarr-py/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ome%2Fome-zarr-py/sbom","scorecard":{"id":706012,"data":{"date":"2025-08-11","repo":{"name":"github.com/ome/ome-zarr-py","commit":"2eec589dbc71cb99712a02c4aa71abdaf8ff39cf"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":4.9,"checks":[{"name":"Maintained","score":10,"reason":"30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Dangerous-Workflow","score":10,"reason":"no dangerous workflow patterns detected","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"Code-Review","score":7,"reason":"Found 3/4 approved changesets -- score normalized to 7","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Warn: no topLevel permission defined: .github/workflows/build.yml:1","Warn: no topLevel permission defined: .github/workflows/codespell.yml:1","Warn: no topLevel permission defined: .github/workflows/dispatch.yml:1","Warn: no topLevel permission defined: .github/workflows/pre.yml:1","Warn: no topLevel permission defined: .github/workflows/publish_pypi.yml:1","Info: no jobLevel write permissions found"],"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Pinned-Dependencies","score":0,"reason":"dependency not pinned by hash detected -- score normalized to 0","details":["Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/build.yml:15: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/build.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/build.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/build.yml:30: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/codespell.yml:17: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/codespell.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/codespell.yml:19: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/codespell.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/dispatch.yml:19: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/dispatch.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/dispatch.yml:24: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/dispatch.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pre.yml:24: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/pre.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pre.yml:26: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/pre.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/pre.yml:49: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/pre.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/publish_pypi.yml:10: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/publish_pypi.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/publish_pypi.yml:11: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/publish_pypi.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/publish_pypi.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/ome/ome-zarr-py/publish_pypi.yml/master?enable=pin","Warn: pipCommand not pinned by hash: .github/workflows/build.yml:24","Warn: pipCommand not pinned by hash: .github/workflows/build.yml:25","Warn: pipCommand not pinned by hash: .github/workflows/pre.yml:42","Warn: pipCommand not pinned by hash: .github/workflows/pre.yml:43","Info:   0 out of   8 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   5 third-party GitHubAction dependencies pinned","Info:   0 out of   4 pipCommand dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"License","score":9,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Warn: project license file does not contain an FSF or OSI license."],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'master'"],"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"Security-Policy","score":9,"reason":"security policy file detected","details":["Info: security policy file detected: github.com/ome/.github/SECURITY.md:1","Info: Found linked content: github.com/ome/.github/SECURITY.md:1","Warn: One or no descriptive hints of disclosure, vulnerability, and/or timelines in security policy","Info: Found text in security policy: github.com/ome/.github/SECURITY.md:1"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Vulnerabilities","score":0,"reason":"14 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: PYSEC-2021-387 / GHSA-j8fq-86c5-5v2r","Warn: Project is vulnerable to: PYSEC-2018-34 / GHSA-2fc2-6r4j-p65h","Warn: Project is vulnerable to: PYSEC-2021-856 / GHSA-5545-2q6w-2gh6","Warn: Project is vulnerable to: PYSEC-2019-108 / GHSA-9fq2-x9r6-wfmf","Warn: Project is vulnerable to: PYSEC-2018-33 / GHSA-cw6w-4rcx-xphc","Warn: Project is vulnerable to: PYSEC-2021-857 / GHSA-f7c7-j99h-c22f","Warn: Project is vulnerable to: GHSA-fpfv-jqm9-f5jm","Warn: Project is vulnerable to: PYSEC-2017-1 / GHSA-frgw-fgh6-9g52","Warn: Project is vulnerable to: PYSEC-2019-156 / GHSA-xp76-357g-9wqq","Warn: Project is vulnerable to: PYSEC-2023-102","Warn: Project is vulnerable to: PYSEC-2023-114","Warn: Project is vulnerable to: PYSEC-2024-48 / GHSA-fj7x-q9j7-g6q6","Warn: Project is vulnerable to: GHSA-6p56-wp2h-9hxr","Warn: Project is vulnerable to: PYSEC-2022-43017 / GHSA-qwmp-2cf2-g9g6"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"Packaging","score":10,"reason":"packaging workflow detected","details":["Info: Project packages its releases by way of GitHub Actions.: .github/workflows/publish_pypi.yml:6"],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"SAST","score":0,"reason":"SAST tool is not run on all commits -- score normalized to 0","details":["Warn: 0 commits out of 30 are checked with a SAST tool"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}}]},"last_synced_at":"2025-08-22T06:36:23.218Z","repository_id":36960993,"created_at":"2025-08-22T06:36:23.218Z","updated_at":"2025-08-22T06:36:23.218Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31793225,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-14T02:24:21.117Z","status":"ssl_error","status_checked_at":"2026-04-14T02:24:20.627Z","response_time":153,"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":["ngff","ome","ome-zarr","zarr"],"created_at":"2024-08-03T09:01:02.156Z","updated_at":"2026-04-14T11:01:22.328Z","avatar_url":"https://github.com/ome.png","language":"Python","funding_links":[],"categories":["Life sciences","Ranked by starred repositories"],"sub_categories":["Kerchunk"],"readme":"|pypi| |docs| |coverage|\n\n===========\nome-zarr-py\n===========\n\nTools for multi-resolution images stored in Zarr filesets, according to the `OME NGFF spec`_.\n\nSee `Documentation \u003chttps://ome-zarr.readthedocs.io/\u003e`_ for usage information.\n\nDocumentation\n-------------\n\nDocumentation will be automatically built with `readthedocs`.\n\nIt can be built locally with::\n\n    $ pip install -r docs/requirements.txt\n    $ sphinx-build -b html docs/source/ docs/build/html\n\nTests\n-----\n\nTests can be run locally via `tox` with::\n\n    $ pip install tox\n    $ tox\n\nTo enable pre-commit code validation::\n\n    $ pip install pre-commit\n    $ pre-commit install\n\nRelease process\n---------------\n\nThis repository uses `setuptools_scm` to manage version numbers.\n\nGo to https://github.com/ome/ome-zarr-py/releases and click on `Draft a new release`.\n\nUnder `Choose a tag`, type the new version number (e.g. `0.1.0`) and choose\n`Create a new tag on publish` from the dropdown.\n\nClick on `Generate release notes` to create a changelog and `Publish release` to publish the release.\n\nLicense\n-------\n\nDistributed under the terms of the `BSD`_ license,\n\"ome-zarr-py\" is free and open source software\n\n.. _`OME NGFF spec`: https://github.com/ome/ngff\n.. _`BSD`: https://opensource.org/licenses/BSD-2-Clause\n\n.. |pypi| image:: https://badge.fury.io/py/ome-zarr.svg\n    :alt: PyPI project\n    :target: https://badge.fury.io/py/ome-zarr\n\n.. |docs| image:: https://readthedocs.org/projects/ome-zarr/badge/?version=stable\n    :alt: Documentation Status\n    :target: https://ome-zarr.readthedocs.io/en/stable/?badge=stable\n\n.. |coverage| image:: https://codecov.io/gh/ome/ome-zarr-py/branch/master/graph/badge.svg\n    :alt: Test coverage\n    :target: https://codecov.io/gh/ome/ome-zarr-py\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fome%2Fome-zarr-py","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fome%2Fome-zarr-py","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fome%2Fome-zarr-py/lists"}