{"id":15600896,"url":"https://github.com/mohamedomar2020/qupath_scripts","last_synced_at":"2025-10-24T20:17:11.226Z","repository":{"id":218547766,"uuid":"746713168","full_name":"MohamedOmar2020/QuPath_scripts","owner":"MohamedOmar2020","description":"Custom groovy scripts for QuaPath","archived":false,"fork":false,"pushed_at":"2024-01-22T14:44:51.000Z","size":9,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-30T10:35:06.792Z","etag":null,"topics":["celltype-annotation","digital-pathology","groovy-script","masked-image-modeling","qupath","qupath-script"],"latest_commit_sha":null,"homepage":"","language":"Groovy","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/MohamedOmar2020.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}},"created_at":"2024-01-22T14:26:49.000Z","updated_at":"2024-01-22T14:42:59.000Z","dependencies_parsed_at":"2024-01-22T18:52:17.074Z","dependency_job_id":null,"html_url":"https://github.com/MohamedOmar2020/QuPath_scripts","commit_stats":null,"previous_names":["mohamedomar2020/qupath_scripts"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/MohamedOmar2020/QuPath_scripts","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MohamedOmar2020%2FQuPath_scripts","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MohamedOmar2020%2FQuPath_scripts/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MohamedOmar2020%2FQuPath_scripts/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MohamedOmar2020%2FQuPath_scripts/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MohamedOmar2020","download_url":"https://codeload.github.com/MohamedOmar2020/QuPath_scripts/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MohamedOmar2020%2FQuPath_scripts/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":275819975,"owners_count":25534813,"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":"2025-09-18T02:00:09.552Z","response_time":77,"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"}},"keywords":["celltype-annotation","digital-pathology","groovy-script","masked-image-modeling","qupath","qupath-script"],"created_at":"2024-10-03T02:07:24.255Z","updated_at":"2025-09-18T19:23:40.035Z","avatar_url":"https://github.com/MohamedOmar2020.png","language":"Groovy","funding_links":[],"categories":[],"sub_categories":[],"readme":"# QuPath Helper Scripts\n\n## Overview\nThis repository contains a collection of Groovy scripts designed to enhance and automate various tasks within QuPath, a powerful open-source software for bioimage analysis, particularly in digital pathology. These scripts are intended to help pathologists and researchers efficiently process and analyze whole slide images (WSIs).\n\n## Scripts Included\n- `CSVtoAnnotations.groovy`: Reads coordinates from a CSV file and creates annotations in QuPath at those locations.\n- `AnnotationColorMapper.groovy`: Applies specific colors to annotations based on their names.\n- `CellTypeMaskGenerator.groovy`: Generates RGB masks from annotated cell types in WSIs, encoding them in the red channel of an RGB mask.\n- (Additional script descriptions as needed)\n\n## Prerequisites\n- [QuPath](https://qupath.github.io/) (Version 0.4.3)\n\n## Installation\nClone or download this repository to your local machine.\n\n## Usage\nEach script in this repository is designed to be run within QuPath's script editor. To use a script:\n1. Open QuPath and load a WSI.\n2. Open the script editor in QuPath (Automate -\u003e Show script editor).\n3. Copy and paste the desired script from this repository into the script editor.\n4. Execute the script.\n\n## Contributing\nContributions to these scripts, including improvements, bug fixes, or additional utility scripts, are welcome. Please feel free to submit pull requests or open issues for discussion.\n\n## License\n[MIT License](LICENSE) - Feel free to use, modify, and distribute these scripts as needed.\n\n## Contact\n- Author: Mohamed Omar, MD\n- Email: mao4005@med.cornell.edu\n- GitHub: https://github.com/MohamedOmar2020\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmohamedomar2020%2Fqupath_scripts","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmohamedomar2020%2Fqupath_scripts","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmohamedomar2020%2Fqupath_scripts/lists"}