{"id":13689019,"url":"https://github.com/brainglobe/brainrender","last_synced_at":"2026-01-12T06:32:37.709Z","repository":{"id":39587490,"uuid":"209513981","full_name":"brainglobe/brainrender","owner":"brainglobe","description":"A Python package to visualise neuroanatomical data in atlas space","archived":false,"fork":false,"pushed_at":"2025-12-02T16:47:54.000Z","size":284300,"stargazers_count":616,"open_issues_count":10,"forks_count":94,"subscribers_count":15,"default_branch":"main","last_synced_at":"2026-01-04T03:03:12.492Z","etag":null,"topics":["anatomy","neuroscience","python","visualization"],"latest_commit_sha":null,"homepage":"https://brainglobe.info/documentation/brainrender/index.html","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/brainglobe.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2019-09-19T09:27:09.000Z","updated_at":"2026-01-01T17:49:13.000Z","dependencies_parsed_at":"2023-01-21T23:05:05.722Z","dependency_job_id":"5daa9aeb-6e4c-4f63-8295-068946ba7e91","html_url":"https://github.com/brainglobe/brainrender","commit_stats":{"total_commits":801,"total_committers":20,"mean_commits":40.05,"dds":"0.31585518102372034","last_synced_commit":"daaa338935e8947b1c249a3fbb650a13f6c69067"},"previous_names":["brancolab/brainrender"],"tags_count":22,"template":false,"template_full_name":null,"purl":"pkg:github/brainglobe/brainrender","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brainglobe%2Fbrainrender","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brainglobe%2Fbrainrender/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brainglobe%2Fbrainrender/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brainglobe%2Fbrainrender/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/brainglobe","download_url":"https://codeload.github.com/brainglobe/brainrender/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brainglobe%2Fbrainrender/sbom","scorecard":{"id":24164,"data":{"date":"2025-08-11","repo":{"name":"github.com/brainglobe/brainrender","commit":"dd731dd5376ccb9d20ed9b81caa3709e94affde6"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":5.5,"checks":[{"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":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Warn: no topLevel permission defined: .github/workflows/test_and_deploy.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":"Maintained","score":4,"reason":"3 commit(s) and 2 issue activity found in the last 90 days -- score normalized to 4","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Code-Review","score":10,"reason":"all changesets reviewed","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":"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":"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":"Vulnerabilities","score":10,"reason":"0 existing vulnerabilities detected","details":null,"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Info: FSF or OSI recognized license: BSD 3-Clause \"New\" or \"Revised\" License: LICENSE:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"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":"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/test_and_deploy.yml:52: update your workflow using https://app.stepsecurity.io/secureworkflow/brainglobe/brainrender/test_and_deploy.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/test_and_deploy.yml:64: update your workflow using https://app.stepsecurity.io/secureworkflow/brainglobe/brainrender/test_and_deploy.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/test_and_deploy.yml:67: update your workflow using https://app.stepsecurity.io/secureworkflow/brainglobe/brainrender/test_and_deploy.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/test_and_deploy.yml:76: update your workflow using https://app.stepsecurity.io/secureworkflow/brainglobe/brainrender/test_and_deploy.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/test_and_deploy.yml:84: update your workflow using https://app.stepsecurity.io/secureworkflow/brainglobe/brainrender/test_and_deploy.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/test_and_deploy.yml:98: update your workflow using https://app.stepsecurity.io/secureworkflow/brainglobe/brainrender/test_and_deploy.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/test_and_deploy.yml:107: update your workflow using https://app.stepsecurity.io/secureworkflow/brainglobe/brainrender/test_and_deploy.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/test_and_deploy.yml:111: update your workflow using https://app.stepsecurity.io/secureworkflow/brainglobe/brainrender/test_and_deploy.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/test_and_deploy.yml:26: update your workflow using https://app.stepsecurity.io/secureworkflow/brainglobe/brainrender/test_and_deploy.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/test_and_deploy.yml:32: update your workflow using https://app.stepsecurity.io/secureworkflow/brainglobe/brainrender/test_and_deploy.yml/main?enable=pin","Info:   0 out of   2 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   8 third-party GitHubAction 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":"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":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"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":"Branch-Protection","score":-1,"reason":"internal error: error during branchesHandler.setup: internal error: githubv4.Query: Resource not accessible by integration","details":null,"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":"Packaging","score":10,"reason":"packaging workflow detected","details":["Info: Project packages its releases by way of GitHub Actions.: .github/workflows/test_and_deploy.yml:101"],"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":"2025-08-14T17:28:08.753Z","repository_id":39587490,"created_at":"2025-08-14T17:28:08.754Z","updated_at":"2025-08-14T17:28:08.754Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28336316,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-12T06:09:07.588Z","status":"ssl_error","status_checked_at":"2026-01-12T06:05:18.301Z","response_time":98,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: 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":["anatomy","neuroscience","python","visualization"],"created_at":"2024-08-02T15:01:30.747Z","updated_at":"2026-01-12T06:32:37.704Z","avatar_url":"https://github.com/brainglobe.png","language":"Python","readme":"# brainrender\n\n*A user-friendly python library to create high-quality, 3D neuro-anatomical renderings combining data from publicly available brain atlases with user-generated experimental data.*\n\n[![Python Version](https://img.shields.io/pypi/pyversions/brainrender.svg)](https://pypi.org/project/brainrender)\n[![PyPI](https://img.shields.io/pypi/v/brainrender.svg)](https://pypi.org/project/brainrender)\n[![tests](https://github.com/brainglobe/brainrender/workflows/tests/badge.svg)](https://github.com/brainglobe/brainrender/actions)\n[![codecov](https://codecov.io/gh/brainglobe/brainrender/graph/badge.svg)](https://codecov.io/gh/brainglobe/brainrender)\n[![Downloads](https://static.pepy.tech/badge/brainrender)](https://pepy.tech/project/brainrender)\n\n\u0026nbsp;\n\u0026nbsp;\n\n![Example gallery](https://iiif.elifesciences.org/lax/65751%2Felife-65751-fig3-v3.tif/full/,1500/0/default.jpg)\n\nFrom: Claudi et al. (2021) Visualizing anatomically registered data with brainrender. eLife\n\n\n## Documentation\n\nbrainrender is a project of the BrainGlobe Initiative, which is a collaborative effort to develop a suite of Python-based software tools for computational neuroanatomy. A comprehensive online documentation for brainrender can be found on the BrainGlobe website [here](https://brainglobe.info/documentation/brainrender/index.html).\n\nFurthermore, an open-access journal article describing BrainRender has been published in eLife, available [here](https://doi.org/10.7554/eLife.65751).\n\n\n## Installation\n\nFrom PyPI:\n\n```\npip install brainrender\n```\n\n## Quickstart\n\n``` python\nimport random\n\nimport numpy as np\n\nfrom brainrender import Scene\nfrom brainrender.actors import Points\n\ndef get_n_random_points_in_region(region, N):\n    \"\"\"\n    Gets N random points inside (or on the surface) of a mesh\n    \"\"\"\n\n    region_bounds = region.mesh.bounds()\n    X = np.random.randint(region_bounds[0], region_bounds[1], size=10000)\n    Y = np.random.randint(region_bounds[2], region_bounds[3], size=10000)\n    Z = np.random.randint(region_bounds[4], region_bounds[5], size=10000)\n    pts = [[x, y, z] for x, y, z in zip(X, Y, Z)]\n\n    ipts = region.mesh.inside_points(pts).coordinates\n    return np.vstack(random.choices(ipts, k=N))\n\n\n# Display the Allen Brain mouse atlas.\nscene = Scene(atlas_name=\"allen_mouse_25um\", title=\"Cells in primary visual cortex\")\n\n# Display a brain region\nprimary_visual = scene.add_brain_region(\"VISp\", alpha=0.2)\n\n# Get a numpy array with (fake) coordinates of some labelled cells\ncoordinates = get_n_random_points_in_region(primary_visual, 2000)\n\n# Create a Points actor\ncells = Points(coordinates)\n\n# Add to scene\nscene.add(cells)\n\n# Add label to the brain region\nscene.add_label(primary_visual, \"Primary visual cortex\")\n\n# Display the figure.\nscene.render()\n\n```\n\n## Seeking help or contributing\nWe are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).\n\n## Citing brainrender\n\nIf you use brainrender in your scientific work, please cite:\n```\nClaudi, F., Tyson, A. L., Petrucco, L., Margrie, T.W., Portugues, R.,  Branco, T. (2021) \"Visualizing anatomically registered data with Brainrender\u0026quot; \u003ci\u003eeLife\u003c/i\u003e 2021;10:e65751 [doi.org/10.7554/eLife.65751](https://doi.org/10.7554/eLife.65751)\n```\n\nBibTeX:\n\n``` bibtex\n@article{Claudi2021,\nauthor = {Claudi, Federico and Tyson, Adam L. and Petrucco, Luigi and Margrie, Troy W. and Portugues, Ruben and Branco, Tiago},\ndoi = {10.7554/eLife.65751},\nissn = {2050084X},\njournal = {eLife},\npages = {1--16},\npmid = {33739286},\ntitle = {{Visualizing anatomically registered data with brainrender}},\nvolume = {10},\nyear = {2021}\n}\n\n```\n","funding_links":[],"categories":["Python","Neuroscience"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrainglobe%2Fbrainrender","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrainglobe%2Fbrainrender","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrainglobe%2Fbrainrender/lists"}