{"id":69561,"name":"SlideRunner","description":"SlideRunner is a tool for massive cell annotations in whole slide images","url":"https://github.com/DeepMicroscopy/SlideRunner","last_synced_at":"2025-09-08T14:54:02.350Z","repository":{"id":40954116,"uuid":"115711597","full_name":"DeepMicroscopy/SlideRunner","owner":"DeepMicroscopy","description":"SlideRunner is a tool for massive cell annotations in whole slide images","archived":false,"fork":false,"pushed_at":"2025-07-29T13:14:36.000Z","size":104527,"stargazers_count":79,"open_issues_count":6,"forks_count":10,"subscribers_count":8,"default_branch":"master","last_synced_at":"2025-08-17T09:26:41.245Z","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":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/DeepMicroscopy.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2017-12-29T10:07:54.000Z","updated_at":"2025-07-29T13:14:40.000Z","dependencies_parsed_at":"2025-07-28T13:24:30.292Z","dependency_job_id":null,"html_url":"https://github.com/DeepMicroscopy/SlideRunner","commit_stats":null,"previous_names":["deepmicroscopy/sliderunner","deeppathology/sliderunner","maubreville/sliderunner"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/DeepMicroscopy/SlideRunner","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DeepMicroscopy%2FSlideRunner","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DeepMicroscopy%2FSlideRunner/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DeepMicroscopy%2FSlideRunner/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DeepMicroscopy%2FSlideRunner/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DeepMicroscopy","download_url":"https://codeload.github.com/DeepMicroscopy/SlideRunner/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DeepMicroscopy%2FSlideRunner/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274202396,"owners_count":25240366,"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":"2025-09-08T02:00:09.813Z","response_time":121,"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":"DeepMicroscopy","name":"DeepMicroscopy - Generating Deep Insights from Deep Learning in Microscopy","uuid":"67414939","kind":"organization","description":"This is our central home for all our digital pathology projects, focusing on deep learning.","email":null,"website":"https://deepmicroscopy.org","location":"Erlangen, Germany","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/67414939?v=4","repositories_count":1,"last_synced_at":"2023-07-10T20:30:37.124Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/DeepMicroscopy","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-03-02T13:30:26.030Z","updated_at":"2023-07-10T20:30:37.126Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DeepMicroscopy","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DeepMicroscopy/repositories"},"packages":[],"commits":{"id":1414935,"full_name":"DeepMicroscopy/SlideRunner","default_branch":"master","committers":[{"name":"Marc Aubreville","email":"marc.aubreville@fau.de","login":null,"count":674},{"name":"Marc Aubreville","email":"marc.aubreville@thi.de","login":null,"count":41},{"name":"Marc Aubreville","email":"marc.aubreville@sivantos.com","login":null,"count":26},{"name":"c.marzahl@de.eu.local","email":"c.marzahl@euroimmun.de","login":null,"count":9},{"name":"wilm","email":"frauke.wilm@fau.de","login":null,"count":7},{"name":"Christian Marzahl","email":"christian.marzahl@gmail.com","login":null,"count":5},{"name":"Marc Aubreville","email":"marc.aubreville@gmail.com","login":null,"count":4},{"name":"dependabot[bot]","email":"49699333+dependabot[bot]","login":"dependabot[bot]","count":3},{"name":"Marc Aubreville","email":"marcaubreville@MacBook-Pro-von-Marc-2.local","login":null,"count":1},{"name":"Robert Klopfleisch","email":"Robert.Klopfleisch@fu-berlin.de","login":null,"count":1},{"name":"Douwe van der Wal","email":"douwe.vanderwal@douwevander-ltm.internal.salesforce.com","login":null,"count":1}],"total_commits":772,"total_committers":11,"total_bot_commits":3,"total_bot_committers":1,"mean_commits":70.18181818181819,"dds":0.12694300518134716,"past_year_committers":[{"name":"dependabot[bot]","email":"49699333+dependabot[bot]","login":"dependabot[bot]","count":1}],"past_year_total_commits":1,"past_year_total_committers":1,"past_year_total_bot_commits":1,"past_year_total_bot_committers":1,"past_year_mean_commits":1.0,"past_year_dds":0.0,"last_synced_at":"2023-10-25T20:01:04.607Z","last_synced_commit":"532bfeb063a7e0e1f22d1816111e508b628436ec","created_at":"2023-10-25T20:00:44.892Z","updated_at":"2023-10-25T20:01:04.608Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/DeepMicroscopy%2FSlideRunner/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:16.827Z","repositories_count":5483992,"commits_count":854420992,"contributors_count":31151709,"owners_count":909079,"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":"DeepMicroscopy/SlideRunner","html_url":"https://github.com/DeepMicroscopy/SlideRunner","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":"2025-08-29T23:24:35.531Z","updated_at":"2025-08-29T23:24:35.531Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/DeepMicroscopy%2FSlideRunner","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/DeepMicroscopy%2FSlideRunner/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":1},"pull_request_author_associations_count":{},"issue_authors":{"hanshuai0911":1},"pull_request_authors":{},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:17.013Z","repositories_count":10167544,"issues_count":32012554,"pull_requests_count":100260947,"authors_count":10729845,"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":{},"past_year_issue_authors":{},"past_year_pull_request_authors":{},"maintainers":[],"active_maintainers":[]},"events":{"total":{"IssuesEvent":1,"WatchEvent":4,"PushEvent":5,"ForkEvent":1},"last_year":{"IssuesEvent":1,"WatchEvent":4,"PushEvent":5,"ForkEvent":1}},"keywords":[],"dependencies":[{"ecosystem":"pypi","filepath":"requirements.txt","sha":null,"kind":"manifest","created_at":"2022-09-19T09:31:35.318Z","updated_at":"2022-09-19T09:31:35.318Z","repository_link":"https://github.com/DeepMicroscopy/SlideRunner/blob/master/requirements.txt","dependencies":[{"id":5412758809,"package_name":"EXCAT_Sync","ecosystem":"pypi","requirements":"==0.0.34","direct":true,"kind":"runtime","optional":false},{"id":5412758813,"package_name":"h5py","ecosystem":"pypi","requirements":"==3.7.0","direct":true,"kind":"runtime","optional":false},{"id":5412758815,"package_name":"matplotlib","ecosystem":"pypi","requirements":"==3.5.3","direct":true,"kind":"runtime","optional":false},{"id":5412758817,"package_name":"numpy","ecosystem":"pypi","requirements":"==1.22.0","direct":true,"kind":"runtime","optional":false},{"id":5412758819,"package_name":"opencv_python","ecosystem":"pypi","requirements":"==4.5.3.56","direct":true,"kind":"runtime","optional":false},{"id":5412758821,"package_name":"openslide_wrapper","ecosystem":"pypi","requirements":"==1.1.2","direct":true,"kind":"runtime","optional":false},{"id":5412758822,"package_name":"Pillow","ecosystem":"pypi","requirements":"==9.2.0","direct":true,"kind":"runtime","optional":false},{"id":5412758824,"package_name":"PyQt5","ecosystem":"pypi","requirements":"==5.15.7","direct":true,"kind":"runtime","optional":false},{"id":5412758826,"package_name":"qt_wsi_registration","ecosystem":"pypi","requirements":"==0.0.11","direct":true,"kind":"runtime","optional":false},{"id":5412758828,"package_name":"requests","ecosystem":"pypi","requirements":"==2.28.1","direct":true,"kind":"runtime","optional":false},{"id":5412758830,"package_name":"requests_toolbelt","ecosystem":"pypi","requirements":"==0.9.1","direct":true,"kind":"runtime","optional":false},{"id":5412758831,"package_name":"rollbar","ecosystem":"pypi","requirements":"==0.14.7","direct":true,"kind":"runtime","optional":false},{"id":5412758833,"package_name":"scikit_image","ecosystem":"pypi","requirements":"==0.16.2","direct":true,"kind":"runtime","optional":false},{"id":5412758835,"package_name":"scikit_learn","ecosystem":"pypi","requirements":"==1.1.2","direct":true,"kind":"runtime","optional":false},{"id":5412758837,"package_name":"scipy","ecosystem":"pypi","requirements":"==1.9.0","direct":true,"kind":"runtime","optional":false},{"id":5412758839,"package_name":"setuptools","ecosystem":"pypi","requirements":"==61.2.0","direct":true,"kind":"runtime","optional":false},{"id":5412758843,"package_name":"Shapely","ecosystem":"pypi","requirements":"==1.8.2","direct":true,"kind":"runtime","optional":false},{"id":5412758845,"package_name":"SlideRunner_dataAccess","ecosystem":"pypi","requirements":"==1.0.9","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"setup.py","sha":null,"kind":"manifest","created_at":"2022-09-19T09:31:35.700Z","updated_at":"2022-09-19T09:31:35.700Z","repository_link":"https://github.com/DeepMicroscopy/SlideRunner/blob/master/setup.py","dependencies":[{"id":5412759403,"package_name":"openslide-python","ecosystem":"pypi","requirements":"\u003e=1.1.1","direct":true,"kind":"runtime","optional":false},{"id":5412759404,"package_name":"opencv-python","ecosystem":"pypi","requirements":"\u003e=3.1.0","direct":true,"kind":"runtime","optional":false},{"id":5412759405,"package_name":"SlideRunner_dataAccess","ecosystem":"pypi","requirements":"\u003e=1.0.7","direct":true,"kind":"runtime","optional":false},{"id":5412759406,"package_name":"matplotlib","ecosystem":"pypi","requirements":"\u003e=2.0.0","direct":true,"kind":"runtime","optional":false},{"id":5412759407,"package_name":"numpy","ecosystem":"pypi","requirements":"\u003e=1.13","direct":true,"kind":"runtime","optional":false},{"id":5412759408,"package_name":"rollbar","ecosystem":"pypi","requirements":"\u003e=0.14","direct":true,"kind":"runtime","optional":false},{"id":5412759409,"package_name":"shapely","ecosystem":"pypi","requirements":"\u003e=1.6.4","direct":true,"kind":"runtime","optional":false},{"id":5412759410,"package_name":"pydicom","ecosystem":"pypi","requirements":"\u003e=1.4.1","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/pythonapp.yml","sha":null,"kind":"manifest","created_at":"2023-01-31T05:15:56.972Z","updated_at":"2023-01-31T05:15:56.972Z","repository_link":"https://github.com/DeepMicroscopy/SlideRunner/blob/master/.github/workflows/pythonapp.yml","dependencies":[{"id":7263513341,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7263513342,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false}]}],"score":6.840546529288687,"created_at":"2025-09-08T11:19:02.610Z","updated_at":"2025-10-07T08:25:47.411Z","avatar_url":"https://github.com/DeepMicroscopy.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1007/978-3-662-56537-7_81","https://doi.org/10.1371/journal.pone.0220074"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["interactive","serializer","cycles","packaging","network-simulation","shellcodes","hacking","autograding","observability","genomics"],"project_url":"https://science.ecosyste.ms/api/v1/projects/69561","html_url":"https://science.ecosyste.ms/projects/69561"}