{"id":42841,"name":"foa3d","description":"A tool for multiscale nerve fiber enhancement and 3D orientation analysis in large high-resolution volumetric brain tissue reconstructions.","url":"https://github.com/lens-biophotonics/foa3d","last_synced_at":"2025-09-05T09:34:04.176Z","repository":{"id":64832654,"uuid":"500358847","full_name":"lens-biophotonics/Foa3D","owner":"lens-biophotonics","description":"A tool for multiscale nerve fiber enhancement and 3D orientation analysis in large high-resolution volumetric brain tissue reconstructions.","archived":false,"fork":false,"pushed_at":"2025-06-30T10:25:53.000Z","size":3240,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-06-30T11:28:50.244Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","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/lens-biophotonics.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","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":"codemeta.json","zenodo":null}},"created_at":"2022-06-06T08:52:45.000Z","updated_at":"2025-06-30T10:25:57.000Z","dependencies_parsed_at":"2023-02-13T00:46:36.574Z","dependency_job_id":"21ef4cc9-d5ab-47c2-940c-13c8113f890c","html_url":"https://github.com/lens-biophotonics/Foa3D","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/lens-biophotonics/Foa3D","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lens-biophotonics%2FFoa3D","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lens-biophotonics%2FFoa3D/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lens-biophotonics%2FFoa3D/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lens-biophotonics%2FFoa3D/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lens-biophotonics","download_url":"https://codeload.github.com/lens-biophotonics/Foa3D/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lens-biophotonics%2FFoa3D/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273739142,"owners_count":25159284,"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","status":"online","status_checked_at":"2025-09-05T02:00:09.113Z","response_time":402,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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"}},"owner":{"login":"lens-biophotonics","name":"lens-biophotonics","uuid":"33419551","kind":"organization","description":"Biophotonics group @ LENS and CNR - INO","email":null,"website":"http://bio.lens.unifi.it/","location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/33419551?v=4","repositories_count":19,"last_synced_at":"2024-04-16T05:44:12.290Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/lens-biophotonics","funding_links":[],"total_stars":59,"followers":6,"following":0,"created_at":"2022-11-11T08:14:13.398Z","updated_at":"2024-04-16T05:44:19.443Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lens-biophotonics","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lens-biophotonics/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"lens-biophotonics/Foa3D","html_url":"https://github.com/lens-biophotonics/Foa3D","last_synced_at":null,"status":null,"issues_count":null,"pull_requests_count":null,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":null,"issues_closed_count":null,"pull_requests_closed_count":null,"pull_request_authors_count":null,"issue_authors_count":null,"avg_comments_per_issue":null,"avg_comments_per_pull_request":null,"merged_pull_requests_count":null,"bot_issues_count":null,"bot_pull_requests_count":null,"past_year_issues_count":null,"past_year_pull_requests_count":null,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":null,"past_year_issues_closed_count":null,"past_year_pull_requests_closed_count":null,"past_year_pull_request_authors_count":null,"past_year_issue_authors_count":null,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":null,"past_year_bot_issues_count":null,"past_year_bot_pull_requests_count":null,"past_year_merged_pull_requests_count":null,"created_at":"2025-08-31T05:30:30.649Z","updated_at":"2025-08-31T06:16:44.981Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/lens-biophotonics%2FFoa3D","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/lens-biophotonics%2FFoa3D/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":1},"pull_request_author_associations_count":{},"issue_authors":{"apdavison":1},"pull_request_authors":{},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10095926,"issues_count":31397479,"pull_requests_count":97150418,"authors_count":10700329,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"NONE":1},"past_year_pull_request_author_associations_count":{},"past_year_issue_authors":{"apdavison":1},"past_year_pull_request_authors":{},"maintainers":[],"active_maintainers":[]},"events":{"total":{"CreateEvent":3,"ReleaseEvent":1,"IssuesEvent":2,"DeleteEvent":2,"IssueCommentEvent":1,"MemberEvent":1,"PushEvent":60},"last_year":{"CreateEvent":3,"ReleaseEvent":1,"IssuesEvent":2,"DeleteEvent":2,"IssueCommentEvent":1,"MemberEvent":1,"PushEvent":60}},"keywords":[],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/python-package-and-doc.yml","sha":null,"kind":"manifest","created_at":"2022-12-15T19:17:14.596Z","updated_at":"2022-12-15T19:17:14.596Z","repository_link":"https://github.com/lens-biophotonics/Foa3D/blob/main/.github/workflows/python-package-and-doc.yml","dependencies":[{"id":6813572505,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":6813572506,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":6813572507,"package_name":"actions/cache","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":6813572508,"package_name":"crazy-max/ghaction-github-pages","ecosystem":"actions","requirements":"v2.2.0","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"pypi","filepath":"requirements-dev.in","sha":null,"kind":"manifest","created_at":"2022-12-15T19:17:26.603Z","updated_at":"2022-12-15T19:17:26.603Z","repository_link":"https://github.com/lens-biophotonics/Foa3D/blob/main/requirements-dev.in","dependencies":[{"id":6813572552,"package_name":"m2r2","ecosystem":"pypi","requirements":"==0.3.2","direct":true,"kind":"development","optional":false},{"id":6813572553,"package_name":"sphinx","ecosystem":"pypi","requirements":"*","direct":true,"kind":"development","optional":false},{"id":6813572554,"package_name":"sphinx_rtd_theme","ecosystem":"pypi","requirements":"*","direct":true,"kind":"development","optional":false},{"id":6813572555,"package_name":"wheel","ecosystem":"pypi","requirements":"*","direct":true,"kind":"development","optional":false}]},{"ecosystem":"pypi","filepath":"requirements-dev.txt","sha":null,"kind":"manifest","created_at":"2022-12-15T19:17:34.811Z","updated_at":"2022-12-15T19:17:34.811Z","repository_link":"https://github.com/lens-biophotonics/Foa3D/blob/main/requirements-dev.txt","dependencies":[{"id":6813572565,"package_name":"alabaster","ecosystem":"pypi","requirements":"==0.7.12","direct":true,"kind":"development","optional":false},{"id":6813572566,"package_name":"babel","ecosystem":"pypi","requirements":"==2.10.3","direct":true,"kind":"development","optional":false},{"id":6813572567,"package_name":"certifi","ecosystem":"pypi","requirements":"==2022.9.24","direct":true,"kind":"development","optional":false},{"id":6813572568,"package_name":"charset-normalizer","ecosystem":"pypi","requirements":"==2.1.1","direct":true,"kind":"development","optional":false},{"id":6813572569,"package_name":"docutils","ecosystem":"pypi","requirements":"==0.17.1","direct":true,"kind":"development","optional":false},{"id":6813572570,"package_name":"idna","ecosystem":"pypi","requirements":"==3.4","direct":true,"kind":"development","optional":false},{"id":6813572571,"package_name":"imagesize","ecosystem":"pypi","requirements":"==1.4.1","direct":true,"kind":"development","optional":false},{"id":6813572572,"package_name":"importlib-metadata","ecosystem":"pypi","requirements":"==5.0.0","direct":true,"kind":"development","optional":false},{"id":6813572573,"package_name":"jinja2","ecosystem":"pypi","requirements":"==3.1.2","direct":true,"kind":"development","optional":false},{"id":6813572574,"package_name":"m2r2","ecosystem":"pypi","requirements":"==0.3.2","direct":true,"kind":"development","optional":false},{"id":6813572575,"package_name":"markupsafe","ecosystem":"pypi","requirements":"==2.1.1","direct":true,"kind":"development","optional":false},{"id":6813572576,"package_name":"mistune","ecosystem":"pypi","requirements":"==0.8.4","direct":true,"kind":"development","optional":false},{"id":6813572577,"package_name":"packaging","ecosystem":"pypi","requirements":"==21.3","direct":true,"kind":"development","optional":false},{"id":6813572578,"package_name":"pygments","ecosystem":"pypi","requirements":"==2.13.0","direct":true,"kind":"development","optional":false},{"id":6813572579,"package_name":"pyparsing","ecosystem":"pypi","requirements":"==3.0.9","direct":true,"kind":"development","optional":false},{"id":6813572580,"package_name":"pytz","ecosystem":"pypi","requirements":"==2022.4","direct":true,"kind":"development","optional":false},{"id":6813572581,"package_name":"requests","ecosystem":"pypi","requirements":"==2.28.1","direct":true,"kind":"development","optional":false},{"id":6813572582,"package_name":"snowballstemmer","ecosystem":"pypi","requirements":"==2.2.0","direct":true,"kind":"development","optional":false},{"id":6813572583,"package_name":"sphinx","ecosystem":"pypi","requirements":"==5.2.3","direct":true,"kind":"development","optional":false},{"id":6813572584,"package_name":"sphinx-rtd-theme","ecosystem":"pypi","requirements":"==1.0.0","direct":true,"kind":"development","optional":false},{"id":6813572585,"package_name":"sphinxcontrib-applehelp","ecosystem":"pypi","requirements":"==1.0.2","direct":true,"kind":"development","optional":false},{"id":6813572586,"package_name":"sphinxcontrib-devhelp","ecosystem":"pypi","requirements":"==1.0.2","direct":true,"kind":"development","optional":false},{"id":6813572587,"package_name":"sphinxcontrib-htmlhelp","ecosystem":"pypi","requirements":"==2.0.0","direct":true,"kind":"development","optional":false},{"id":6813572588,"package_name":"sphinxcontrib-jsmath","ecosystem":"pypi","requirements":"==1.0.1","direct":true,"kind":"development","optional":false},{"id":6813572589,"package_name":"sphinxcontrib-qthelp","ecosystem":"pypi","requirements":"==1.0.3","direct":true,"kind":"development","optional":false},{"id":6813572590,"package_name":"sphinxcontrib-serializinghtml","ecosystem":"pypi","requirements":"==1.1.5","direct":true,"kind":"development","optional":false},{"id":6813572591,"package_name":"urllib3","ecosystem":"pypi","requirements":"==1.26.12","direct":true,"kind":"development","optional":false},{"id":6813572592,"package_name":"wheel","ecosystem":"pypi","requirements":"==0.37.1","direct":true,"kind":"development","optional":false},{"id":6813572593,"package_name":"zipp","ecosystem":"pypi","requirements":"==3.8.1","direct":true,"kind":"development","optional":false}]},{"ecosystem":"pypi","filepath":"requirements.in","sha":null,"kind":"manifest","created_at":"2022-12-15T19:17:45.819Z","updated_at":"2022-12-15T19:17:45.819Z","repository_link":"https://github.com/lens-biophotonics/Foa3D/blob/main/requirements.in","dependencies":[{"id":6813572606,"package_name":"alive-progress","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":6813572607,"package_name":"astropy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":6813572608,"package_name":"h5py","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":6813572609,"package_name":"matplotlib","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":6813572610,"package_name":"nibabel","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":6813572611,"package_name":"numba","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":6813572612,"package_name":"scikit-image","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"requirements.txt","sha":null,"kind":"lockfile","created_at":"2022-12-15T19:17:54.525Z","updated_at":"2022-12-15T19:17:54.525Z","repository_link":"https://github.com/lens-biophotonics/Foa3D/blob/main/requirements.txt","dependencies":[{"id":6813572755,"package_name":"about-time","ecosystem":"pypi","requirements":"==3.1.1","direct":false,"kind":"runtime","optional":false},{"id":6813572756,"package_name":"alive-progress","ecosystem":"pypi","requirements":"==2.4.1","direct":false,"kind":"runtime","optional":false},{"id":6813572757,"package_name":"astropy","ecosystem":"pypi","requirements":"==5.1","direct":false,"kind":"runtime","optional":false},{"id":6813572758,"package_name":"contourpy","ecosystem":"pypi","requirements":"==1.0.5","direct":false,"kind":"runtime","optional":false},{"id":6813572759,"package_name":"cycler","ecosystem":"pypi","requirements":"==0.11.0","direct":false,"kind":"runtime","optional":false},{"id":6813572760,"package_name":"fonttools","ecosystem":"pypi","requirements":"==4.37.4","direct":false,"kind":"runtime","optional":false},{"id":6813572761,"package_name":"grapheme","ecosystem":"pypi","requirements":"==0.6.0","direct":false,"kind":"runtime","optional":false},{"id":6813572762,"package_name":"h5py","ecosystem":"pypi","requirements":"==3.7.0","direct":false,"kind":"runtime","optional":false},{"id":6813572763,"package_name":"imageio","ecosystem":"pypi","requirements":"==2.22.1","direct":false,"kind":"runtime","optional":false},{"id":6813572764,"package_name":"importlib-metadata","ecosystem":"pypi","requirements":"==5.0.0","direct":false,"kind":"runtime","optional":false},{"id":6813572765,"package_name":"kiwisolver","ecosystem":"pypi","requirements":"==1.4.4","direct":false,"kind":"runtime","optional":false},{"id":6813572766,"package_name":"llvmlite","ecosystem":"pypi","requirements":"==0.39.1","direct":false,"kind":"runtime","optional":false},{"id":6813572767,"package_name":"matplotlib","ecosystem":"pypi","requirements":"==3.6.0","direct":false,"kind":"runtime","optional":false},{"id":6813572768,"package_name":"networkx","ecosystem":"pypi","requirements":"==2.8.7","direct":false,"kind":"runtime","optional":false},{"id":6813572769,"package_name":"nibabel","ecosystem":"pypi","requirements":"==4.0.2","direct":false,"kind":"runtime","optional":false},{"id":6813572770,"package_name":"numba","ecosystem":"pypi","requirements":"==0.56.2","direct":false,"kind":"runtime","optional":false},{"id":6813572771,"package_name":"numpy","ecosystem":"pypi","requirements":"==1.23.3","direct":false,"kind":"runtime","optional":false},{"id":6813572772,"package_name":"packaging","ecosystem":"pypi","requirements":"==21.3","direct":false,"kind":"runtime","optional":false},{"id":6813572773,"package_name":"pillow","ecosystem":"pypi","requirements":"==9.2.0","direct":false,"kind":"runtime","optional":false},{"id":6813572774,"package_name":"pyerfa","ecosystem":"pypi","requirements":"==2.0.0.1","direct":false,"kind":"runtime","optional":false},{"id":6813572775,"package_name":"pyparsing","ecosystem":"pypi","requirements":"==3.0.9","direct":false,"kind":"runtime","optional":false},{"id":6813572776,"package_name":"python-dateutil","ecosystem":"pypi","requirements":"==2.8.2","direct":false,"kind":"runtime","optional":false},{"id":6813572777,"package_name":"pywavelets","ecosystem":"pypi","requirements":"==1.4.1","direct":false,"kind":"runtime","optional":false},{"id":6813572778,"package_name":"pyyaml","ecosystem":"pypi","requirements":"==6.0","direct":false,"kind":"runtime","optional":false},{"id":6813572779,"package_name":"scikit-image","ecosystem":"pypi","requirements":"==0.19.3","direct":false,"kind":"runtime","optional":false},{"id":6813572780,"package_name":"scipy","ecosystem":"pypi","requirements":"==1.9.1","direct":false,"kind":"runtime","optional":false},{"id":6813572781,"package_name":"six","ecosystem":"pypi","requirements":"==1.16.0","direct":false,"kind":"runtime","optional":false},{"id":6813572782,"package_name":"tifffile","ecosystem":"pypi","requirements":"==2022.8.12","direct":false,"kind":"runtime","optional":false},{"id":6813572783,"package_name":"zipp","ecosystem":"pypi","requirements":"==3.8.1","direct":false,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-04T15:51:17.797Z","updated_at":"2025-11-04T15:57:10.960Z","avatar_url":"https://github.com/lens-biophotonics.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1038/s41598-023-30953-w","https://doi.org/10.1016/j.media.2020.101760","https://doi.org/10.1007/BFb0056195"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/42841","html_url":"https://science.ecosyste.ms/projects/42841"}