{"id":43298,"name":"exllsm-circuit-reconstruction","description":"Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery","url":"https://github.com/janeliascicomp/exllsm-circuit-reconstruction","last_synced_at":"2025-09-05T09:46:24.760Z","repository":{"id":78049238,"uuid":"323991895","full_name":"JaneliaSciComp/exllsm-circuit-reconstruction","owner":"JaneliaSciComp","description":"Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery","archived":false,"fork":false,"pushed_at":"2025-04-10T15:03:01.000Z","size":1304,"stargazers_count":13,"open_issues_count":2,"forks_count":1,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-06-02T07:20:21.482Z","etag":null,"topics":["image-processing","lightsheet","machine-learning","microscopy","neuroscience","nextflow-pipelines","pipeline","segmentation"],"latest_commit_sha":null,"homepage":"","language":"Nextflow","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/JaneliaSciComp.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}},"created_at":"2020-12-23T20:05:05.000Z","updated_at":"2025-04-10T15:03:06.000Z","dependencies_parsed_at":"2024-11-08T14:24:05.599Z","dependency_job_id":"554d7f2d-9854-4cc1-8c80-780667a895bc","html_url":"https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction","commit_stats":null,"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"purl":"pkg:github/JaneliaSciComp/exllsm-circuit-reconstruction","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fexllsm-circuit-reconstruction","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fexllsm-circuit-reconstruction/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fexllsm-circuit-reconstruction/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fexllsm-circuit-reconstruction/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JaneliaSciComp","download_url":"https://codeload.github.com/JaneliaSciComp/exllsm-circuit-reconstruction/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fexllsm-circuit-reconstruction/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273740476,"owners_count":25159432,"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":"JaneliaSciComp","name":"Howard Hughes Medical Institute","uuid":"1020012","kind":"organization","description":"GitHub organization maintained by Scientific Computing Software at HHMI's Janelia Research Campus for use by HHMI staff and external collaborators.","email":null,"website":"http://www.janelia.org","location":"19700 Helix Drive, Ashburn, VA 20147","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/1020012?v=4","repositories_count":248,"last_synced_at":"2024-04-07T00:42:58.163Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/JaneliaSciComp","funding_links":[],"total_stars":620,"followers":65,"following":0,"created_at":"2022-11-02T21:29:34.858Z","updated_at":"2024-04-07T00:43:46.001Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JaneliaSciComp","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JaneliaSciComp/repositories"},"packages":[],"commits":{"id":4563787,"full_name":"janeliascicomp/exllsm-circuit-reconstruction","default_branch":"master","committers":[{"name":"Cristian Goina","email":"goinac@hhmi.org","login":null,"count":694},{"name":"josh lillvis","email":"lillvis","login":"lillvis","count":157},{"name":"Konrad Rokicki","email":"rokickik@janelia.hhmi.org","login":"krokicki","count":98},{"name":"Cristian Goina","email":"goinac@janelia.hhmi.org","login":"cgoina","count":40},{"name":"takashi310","email":"kawaset@kawaset-ws2.hhmi.org","login":null,"count":3}],"total_commits":992,"total_committers":5,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":198.4,"dds":0.3004032258064516,"past_year_committers":[{"name":"takashi310","email":"kawaset@kawaset-ws2.hhmi.org","login":null,"count":3},{"name":"Cristian Goina","email":"goinac@hhmi.org","login":null,"count":1}],"past_year_total_commits":4,"past_year_total_committers":2,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":2.0,"past_year_dds":0.25,"last_synced_at":"2025-06-01T22:17:28.054Z","last_synced_commit":"2d314b7fe2eed7cab5a001fef894528a3406e988","created_at":"2024-11-08T14:23:14.437Z","updated_at":"2025-06-01T22:17:28.054Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/janeliascicomp%2Fexllsm-circuit-reconstruction/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.343Z","repositories_count":5480019,"commits_count":853389012,"contributors_count":31098138,"owners_count":906558,"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":"janeliascicomp/exllsm-circuit-reconstruction","html_url":"https://github.com/janeliascicomp/exllsm-circuit-reconstruction","last_synced_at":"2025-08-31T12:19:52.712Z","status":null,"issues_count":2,"pull_requests_count":5,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":219185.0,"issues_closed_count":0,"pull_requests_closed_count":4,"pull_request_authors_count":1,"issue_authors_count":1,"avg_comments_per_issue":1.0,"avg_comments_per_pull_request":0.0,"merged_pull_requests_count":4,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":0,"past_year_pull_requests_count":5,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":219185.0,"past_year_issues_closed_count":0,"past_year_pull_requests_closed_count":4,"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":4,"created_at":"2024-11-08T14:23:15.240Z","updated_at":"2025-09-03T03:28:50.751Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/janeliascicomp%2Fexllsm-circuit-reconstruction","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/janeliascicomp%2Fexllsm-circuit-reconstruction/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":2},"pull_request_author_associations_count":{"NONE":6},"issue_authors":{"piotrsan":2},"pull_request_authors":{"takashi310":6},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10086255,"issues_count":31275313,"pull_requests_count":96382867,"authors_count":10695584,"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":{"NONE":6},"past_year_issue_authors":{},"past_year_pull_request_authors":{"takashi310":6},"maintainers":[],"active_maintainers":[]},"events":{"total":{"WatchEvent":1,"PushEvent":3,"PullRequestEvent":5,"ForkEvent":1},"last_year":{"WatchEvent":1,"PushEvent":3,"PullRequestEvent":5,"ForkEvent":1}},"keywords":["image-processing","lightsheet","machine-learning","microscopy","neuroscience","nextflow-pipelines","pipeline","segmentation"],"dependencies":[{"ecosystem":"docker","filepath":"containers/image-processing/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-03-07T22:45:31.378Z","updated_at":"2023-03-07T22:45:31.378Z","repository_link":"https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction/blob/master/containers/image-processing/Dockerfile","dependencies":[{"id":8059902515,"package_name":"janeliascicomp/builder","ecosystem":"docker","requirements":"1.2.1","direct":true,"kind":"build","optional":false},{"id":8059902563,"package_name":"janeliascicomp/fiji-zulu-8","ecosystem":"docker","requirements":"20201021-2016","direct":true,"kind":"build","optional":false}]},{"ecosystem":"docker","filepath":"containers/n5-spark-tools/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-03-07T22:45:31.543Z","updated_at":"2023-03-07T22:45:31.543Z","repository_link":"https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction/blob/master/containers/n5-spark-tools/Dockerfile","dependencies":[{"id":8059903181,"package_name":"janeliascicomp/builder","ecosystem":"docker","requirements":"1.2.1","direct":true,"kind":"build","optional":false},{"id":8059903182,"package_name":"multifish/spark","ecosystem":"docker","requirements":"3.0.1-hadoop3.2","direct":true,"kind":"build","optional":false}]},{"ecosystem":"docker","filepath":"containers/neuron-segmentation/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-03-07T22:45:31.655Z","updated_at":"2023-03-07T22:45:31.655Z","repository_link":"https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction/blob/master/containers/neuron-segmentation/Dockerfile","dependencies":[{"id":8059903420,"package_name":"janeliascicomp/builder","ecosystem":"docker","requirements":"1.2.1","direct":true,"kind":"build","optional":false},{"id":8059903421,"package_name":"condaforge/mambaforge","ecosystem":"docker","requirements":"latest","direct":true,"kind":"build","optional":false}]},{"ecosystem":"docker","filepath":"containers/stitching/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-03-07T22:45:31.736Z","updated_at":"2023-03-07T22:45:31.736Z","repository_link":"https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction/blob/master/containers/stitching/Dockerfile","dependencies":[{"id":8059903637,"package_name":"janeliascicomp/builder","ecosystem":"docker","requirements":"1.2.1","direct":true,"kind":"build","optional":false},{"id":8059903638,"package_name":"multifish/spark","ecosystem":"docker","requirements":"3.0.1-hadoop3.2","direct":true,"kind":"build","optional":false}]},{"ecosystem":"docker","filepath":"containers/synapse/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-03-07T22:45:31.813Z","updated_at":"2023-03-07T22:45:31.813Z","repository_link":"https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction/blob/master/containers/synapse/Dockerfile","dependencies":[{"id":8059903845,"package_name":"janeliascicomp/builder","ecosystem":"docker","requirements":"1.2.1","direct":true,"kind":"build","optional":false},{"id":8059903846,"package_name":"janeliascicomp/matlab-oraclelinux8","ecosystem":"docker","requirements":"2020b","direct":true,"kind":"build","optional":false},{"id":8059903847,"package_name":"oraclelinux","ecosystem":"docker","requirements":"8","direct":true,"kind":"build","optional":false}]},{"ecosystem":"docker","filepath":"containers/synapse-dask/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-03-07T22:45:31.879Z","updated_at":"2023-03-07T22:45:31.879Z","repository_link":"https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction/blob/master/containers/synapse-dask/Dockerfile","dependencies":[{"id":8059904160,"package_name":"condaforge/mambaforge","ecosystem":"docker","requirements":"latest","direct":true,"kind":"build","optional":false}]}],"score":4.31748811353631,"created_at":"2025-09-04T15:51:18.335Z","updated_at":"2025-10-07T08:17:33.012Z","avatar_url":"https://github.com/JaneliaSciComp.png","language":"Nextflow","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.7554/eLife.81248"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/43298","html_url":"https://science.ecosyste.ms/projects/43298","bibtex_url":"https://science.ecosyste.ms/projects/43298/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/43298/export.apalike"}