{"id":37496,"name":"image-st","description":"A pipeline to generate count matrix for different spatial technologies. ISS/MERFISH-like data are decoded using PoSTcode","url":"https://github.com/cellgeni/image-st","last_synced_at":"2025-09-05T07:26:50.437Z","repository":{"id":255339949,"uuid":"849268509","full_name":"cellgeni/Image-ST","owner":"cellgeni","description":"A pipeline to generate count matrix for different spatial technologies. ISS/MERFISH-like data are decoded using PoSTcode","archived":false,"fork":false,"pushed_at":"2025-08-05T19:39:20.000Z","size":1437,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-08-05T21:29:38.933Z","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/cellgeni.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":"2024-08-29T09:38:32.000Z","updated_at":"2025-08-05T19:39:23.000Z","dependencies_parsed_at":"2025-08-05T21:16:12.563Z","dependency_job_id":"27513605-8bb8-4db3-9d69-280200b9809c","html_url":"https://github.com/cellgeni/Image-ST","commit_stats":null,"previous_names":["cellgeni/image-st"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/cellgeni/Image-ST","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2FImage-ST","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2FImage-ST/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2FImage-ST/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2FImage-ST/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cellgeni","download_url":"https://codeload.github.com/cellgeni/Image-ST/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2FImage-ST/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273726321,"owners_count":25156913,"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":"cellgeni","name":"Cellular Genetics Informatics","uuid":"34610939","kind":"organization","description":"Wellcome Sanger Institute","email":null,"website":"https://www.sanger.ac.uk/science/groups/cellular-genetics-informatics","location":"United Kingdom","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/34610939?v=4","repositories_count":19,"last_synced_at":"2023-03-09T02:36:33.917Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/cellgeni","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-18T16:01:46.525Z","updated_at":"2023-03-09T02:36:33.989Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cellgeni","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cellgeni/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"cellgeni/Image-ST","html_url":"https://github.com/cellgeni/Image-ST","last_synced_at":"2025-08-31T13:29:46.049Z","status":null,"issues_count":0,"pull_requests_count":4,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":716665.5,"issues_closed_count":0,"pull_requests_closed_count":4,"pull_request_authors_count":1,"issue_authors_count":0,"avg_comments_per_issue":null,"avg_comments_per_pull_request":0.0,"merged_pull_requests_count":3,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":0,"past_year_pull_requests_count":4,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":716665.5,"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":3,"created_at":"2025-08-30T13:13:41.252Z","updated_at":"2025-09-02T10:44:33.901Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2FImage-ST","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2FImage-ST/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{},"pull_request_author_associations_count":{"COLLABORATOR":4},"issue_authors":{},"pull_request_authors":{"BioinfoTongLI":4},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10087320,"issues_count":31306968,"pull_requests_count":96469683,"authors_count":10696025,"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":4},"past_year_issue_authors":{},"past_year_pull_request_authors":{"BioinfoTongLI":4},"maintainers":[{"login":"BioinfoTongLI","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/BioinfoTongLI"}],"active_maintainers":[{"login":"BioinfoTongLI","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/BioinfoTongLI"}]},"events":{"total":{"WatchEvent":1,"PushEvent":37,"PullRequestEvent":8},"last_year":{"WatchEvent":1,"PushEvent":37,"PullRequestEvent":8}},"keywords":[],"dependencies":[{"ecosystem":"cpan","filepath":"modules/sanger-cellgeni/imaging/cellpose/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.098Z","updated_at":"2025-08-05T21:16:07.098Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/cellpose/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/sanger-cellgeni/imaging/concatenatewkts/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.161Z","updated_at":"2025-08-05T21:16:07.161Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/concatenatewkts/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/sanger-cellgeni/imaging/deepcell/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.230Z","updated_at":"2025-08-05T21:16:07.230Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/deepcell/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/sanger-cellgeni/imaging/extractpeakprofile/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.294Z","updated_at":"2025-08-05T21:16:07.294Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/extractpeakprofile/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/sanger-cellgeni/imaging/generatetiles/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.349Z","updated_at":"2025-08-05T21:16:07.349Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/generatetiles/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/sanger-cellgeni/imaging/instanseg/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.407Z","updated_at":"2025-08-05T21:16:07.407Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/instanseg/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/sanger-cellgeni/imaging/mergeoutlines/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.461Z","updated_at":"2025-08-05T21:16:07.461Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/mergeoutlines/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/sanger-cellgeni/imaging/mergepeaks/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.531Z","updated_at":"2025-08-05T21:16:07.531Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/mergepeaks/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/sanger-cellgeni/imaging/microaligner/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.590Z","updated_at":"2025-08-05T21:16:07.590Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/microaligner/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/sanger-cellgeni/imaging/postcode/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.645Z","updated_at":"2025-08-05T21:16:07.645Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/postcode/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/sanger-cellgeni/imaging/stardist/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.700Z","updated_at":"2025-08-05T21:16:07.700Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/stardist/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/sanger-cellgeni/imaging/tiledspotiflow/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.755Z","updated_at":"2025-08-05T21:16:07.755Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/tiledspotiflow/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/sanger-cellgeni/microaligner_registration/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.837Z","updated_at":"2025-08-05T21:16:07.837Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/subworkflows/sanger-cellgeni/microaligner_registration/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/sanger-cellgeni/tiled_segmentation/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.891Z","updated_at":"2025-08-05T21:16:07.891Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/subworkflows/sanger-cellgeni/tiled_segmentation/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/sanger-cellgeni/tiled_spotiflow/meta.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:07.958Z","updated_at":"2025-08-05T21:16:07.958Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/subworkflows/sanger-cellgeni/tiled_spotiflow/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/sanger-cellgeni/imaging/deepcell/environment.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:08.035Z","updated_at":"2025-08-05T21:16:08.035Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/deepcell/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/sanger-cellgeni/imaging/instanseg/environment.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:08.089Z","updated_at":"2025-08-05T21:16:08.089Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/instanseg/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/sanger-cellgeni/imaging/stardist/environment.yml","sha":null,"kind":"manifest","created_at":"2025-08-05T21:16:08.145Z","updated_at":"2025-08-05T21:16:08.145Z","repository_link":"https://github.com/cellgeni/Image-ST/blob/main/modules/sanger-cellgeni/imaging/stardist/environment.yml","dependencies":[]}],"score":null,"created_at":"2025-09-04T15:51:11.258Z","updated_at":"2025-10-07T08:15:25.923Z","avatar_url":"https://github.com/cellgeni.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":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/37496","html_url":"https://science.ecosyste.ms/projects/37496","bibtex_url":"https://science.ecosyste.ms/projects/37496/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/37496/export.apalike"}