{"id":104122,"name":null,"description":"Pipelines and modules for processing optical physiology data","url":"https://github.com/alleninstitute/ophys_etl_pipelines","last_synced_at":"2025-09-09T03:57:37.275Z","repository":{"id":37951024,"uuid":"274240166","full_name":"AllenInstitute/ophys_etl_pipelines","owner":"AllenInstitute","description":"Pipelines and modules for processing optical physiology data","archived":false,"fork":false,"pushed_at":"2024-12-20T18:25:40.000Z","size":31098,"stargazers_count":11,"open_issues_count":78,"forks_count":5,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-04-11T20:11:33.394Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/AllenInstitute.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","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":null,"zenodo":null}},"created_at":"2020-06-22T20:54:32.000Z","updated_at":"2025-02-03T23:53:57.000Z","dependencies_parsed_at":"2025-04-11T20:20:57.862Z","dependency_job_id":null,"html_url":"https://github.com/AllenInstitute/ophys_etl_pipelines","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/AllenInstitute/ophys_etl_pipelines","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fophys_etl_pipelines","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fophys_etl_pipelines/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fophys_etl_pipelines/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fophys_etl_pipelines/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AllenInstitute","download_url":"https://codeload.github.com/AllenInstitute/ophys_etl_pipelines/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fophys_etl_pipelines/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274241416,"owners_count":25247800,"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":"2025-09-09T02:00:10.223Z","response_time":80,"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":"AllenInstitute","name":"Allen Institute","uuid":"1848392","kind":"organization","description":"Please visit http://alleninstitute.github.io/ for more information.","email":null,"website":"https://alleninstitute.org","location":"Seattle, WA","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/1848392?v=4","repositories_count":184,"last_synced_at":"2023-03-22T17:11:50.580Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/AllenInstitute","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-03T11:18:51.640Z","updated_at":"2023-03-22T17:11:51.155Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AllenInstitute","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AllenInstitute/repositories"},"packages":null,"commits":{"id":7451138,"full_name":"alleninstitute/ophys_etl_pipelines","default_branch":"main","committers":[{"name":"danielsf","email":"scott.daniel@alleninstitute.org","login":"danielsf","count":608},{"name":"Dan","email":"danielk@alleninstitute.org","login":"djkapner","count":206},{"name":"Jed Perkins","email":"perkins.jed@gmail.com","login":"JFPerkins","count":66},{"name":"Mike Huang","email":"huangjmike@gmail.com","login":"mikejhuang","count":53},{"name":"Nicholas Mei","email":"nicholas.mei@alleninstitute.org","login":"njmei","count":48},{"name":"Christopher B. Morrison","email":"chris.morrison@alleninstitute.org","login":"morriscb","count":29},{"name":"Kat Schelonka","email":"kschelon@gmail.com","login":"kschelonka","count":25},{"name":"Adam Amster","email":"adam.amster@alleninstitute.org","login":"aamster","count":22},{"name":"matyasz","email":"tjmatyasz@gmail.com","login":"Matyasz","count":21},{"name":"samiamseid","email":"sams@alleninstitute.org","login":"samiamseid","count":16},{"name":"ross hytnen","email":"rossh@alleninstitute.org","login":"rhytnen","count":3},{"name":"isaak-willett","email":"58192697+isaak-willett","login":"isaak-willett","count":2}],"total_commits":1099,"total_committers":12,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":91.58333333333333,"dds":0.44676979071883527,"past_year_committers":[{"name":"samiamseid","email":"sams@alleninstitute.org","login":"samiamseid","count":15}],"past_year_total_commits":15,"past_year_total_committers":1,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":15.0,"past_year_dds":0.0,"last_synced_at":"2025-04-15T23:41:05.342Z","last_synced_commit":"9d35cb9bfe1120d0686c2af477737621bc90dda7","created_at":"2024-12-09T02:16:29.557Z","updated_at":"2025-04-15T23:41:06.620Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/alleninstitute%2Fophys_etl_pipelines/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-09T00:17:06.873Z","repositories_count":5504463,"commits_count":856928083,"contributors_count":31336895,"owners_count":914237,"icon_url":"https://github.com/github.png","host_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories"}},"issues_stats":{"full_name":"alleninstitute/ophys_etl_pipelines","html_url":"https://github.com/alleninstitute/ophys_etl_pipelines","last_synced_at":"2025-04-11T20:10:55.234Z","status":null,"issues_count":88,"pull_requests_count":94,"avg_time_to_close_issue":2872516.869047619,"avg_time_to_close_pull_request":332104.62765957444,"issues_closed_count":84,"pull_requests_closed_count":94,"pull_request_authors_count":6,"issue_authors_count":5,"avg_comments_per_issue":2.25,"avg_comments_per_pull_request":1.627659574468085,"merged_pull_requests_count":78,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":0,"past_year_pull_requests_count":2,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":8.0,"past_year_issues_closed_count":0,"past_year_pull_requests_closed_count":2,"past_year_pull_request_authors_count":1,"past_year_issue_authors_count":0,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":0.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":2,"created_at":"2024-12-09T02:16:33.410Z","updated_at":"2025-09-03T05:01:15.978Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/alleninstitute%2Fophys_etl_pipelines","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/alleninstitute%2Fophys_etl_pipelines/issues","issue_labels_count":{"wontfix":1,"bug":1,"Epic":1},"pull_request_labels_count":{"dependencies":1},"issue_author_associations_count":{"CONTRIBUTOR":31,"NONE":19},"pull_request_author_associations_count":{"CONTRIBUTOR":50,"COLLABORATOR":9,"NONE":1},"issue_authors":{"wbwakeman":19,"djkapner":15,"pickles-bread-and-butter":7,"njmei":7,"kschelonka":2},"pull_request_authors":{"djkapner":24,"njmei":18,"samiamseid":9,"kschelonka":5,"pickles-bread-and-butter":2,"dependabot[bot]":1,"Matyasz":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-09T00:00:11.778Z","repositories_count":10175542,"issues_count":31894846,"pull_requests_count":99980946,"authors_count":10735096,"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":{},"past_year_pull_request_author_associations_count":{"COLLABORATOR":3},"past_year_issue_authors":{},"past_year_pull_request_authors":{"samiamseid":3},"maintainers":[{"login":"samiamseid","count":9,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/samiamseid"}],"active_maintainers":[{"login":"samiamseid","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/samiamseid"}]},"events":{"total":{"WatchEvent":2,"PushEvent":4,"PullRequestEvent":4,"CreateEvent":1},"last_year":{"WatchEvent":2,"PushEvent":4,"PullRequestEvent":4,"CreateEvent":1}},"keywords":[],"dependencies":[{"ecosystem":"pypi","filepath":"requirements.txt","sha":null,"kind":"manifest","created_at":"2022-08-09T21:40:11.529Z","updated_at":"2022-08-09T21:40:11.529Z","repository_link":"https://github.com/AllenInstitute/ophys_etl_pipelines/blob/main/requirements.txt","dependencies":[{"id":958262867,"package_name":"numpy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262868,"package_name":"scipy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262869,"package_name":"imageio-ffmpeg","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262870,"package_name":"pytest","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262871,"package_name":"coverage","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262872,"package_name":"argschema","ecosystem":"pypi","requirements":"==2.0.2","direct":true,"kind":"runtime","optional":false},{"id":958262873,"package_name":"h5py","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262874,"package_name":"matplotlib","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262875,"package_name":"pandas","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262876,"package_name":"moto","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262877,"package_name":"boto3","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262878,"package_name":"croissant-ml","ecosystem":"pypi","requirements":"==0.0.3","direct":true,"kind":"runtime","optional":false},{"id":958262879,"package_name":"typing_extensions","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262880,"package_name":"tifffile","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262881,"package_name":"scikit-image","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262882,"package_name":"networkx","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":958262883,"package_name":"suite2p","ecosystem":"pypi","requirements":"==0.10.2","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"docker","filepath":".circleci/docker/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-10-13T11:30:03.333Z","updated_at":"2023-10-13T11:30:03.333Z","repository_link":"https://github.com/AllenInstitute/ophys_etl_pipelines/blob/main/.circleci/docker/Dockerfile","dependencies":[{"id":14192869315,"package_name":"continuumio/miniconda3","ecosystem":"docker","requirements":"4.8.2","direct":true,"kind":"build","optional":false}]},{"ecosystem":"docker","filepath":"docker/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-10-13T11:30:03.579Z","updated_at":"2023-10-13T11:30:03.579Z","repository_link":"https://github.com/AllenInstitute/ophys_etl_pipelines/blob/main/docker/Dockerfile","dependencies":[{"id":14192869927,"package_name":"continuumio/miniconda3","ecosystem":"docker","requirements":"4.8.2","direct":true,"kind":"build","optional":false}]},{"ecosystem":"pypi","filepath":"setup.py","sha":null,"kind":"manifest","created_at":"2023-10-13T11:30:03.736Z","updated_at":"2023-10-13T11:30:03.736Z","repository_link":"https://github.com/AllenInstitute/ophys_etl_pipelines/blob/main/setup.py","dependencies":[]}],"score":6.9735430195201396,"created_at":"2025-09-08T22:18:54.067Z","updated_at":"2025-10-07T08:31:29.052Z","avatar_url":"https://github.com/AllenInstitute.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["bioinformatics"],"project_url":"https://science.ecosyste.ms/api/v1/projects/104122","html_url":"https://science.ecosyste.ms/projects/104122"}