{"id":50349477,"url":"https://github.com/sbalci/qupath-extension-workshop","last_synced_at":"2026-05-29T20:30:30.752Z","repository":{"id":358972268,"uuid":"1240697127","full_name":"sbalci/qupath-extension-workshop","owner":"sbalci","description":"QuPath Atölye Scriptleri — Patologlar için QuPath workshop'unun yedi Groovy scriptini tek-tıkla menü olarak paketleyen QuPath uzantısı.","archived":false,"fork":false,"pushed_at":"2026-05-27T17:35:28.000Z","size":348,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-05-27T19:23:38.020Z","etag":null,"topics":["image","image-analysis","pathology","plugin","qupath","workshop"],"latest_commit_sha":null,"homepage":"https://atolye.patoloji.dev/","language":"Groovy","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/sbalci.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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-05-16T13:04:07.000Z","updated_at":"2026-05-27T17:35:32.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/sbalci/qupath-extension-workshop","commit_stats":null,"previous_names":["sbalci/qupath-extension-workshop"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/sbalci/qupath-extension-workshop","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbalci%2Fqupath-extension-workshop","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbalci%2Fqupath-extension-workshop/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbalci%2Fqupath-extension-workshop/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbalci%2Fqupath-extension-workshop/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sbalci","download_url":"https://codeload.github.com/sbalci/qupath-extension-workshop/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbalci%2Fqupath-extension-workshop/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33670211,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-05-29T02:00:06.066Z","response_time":107,"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":["image","image-analysis","pathology","plugin","qupath","workshop"],"created_at":"2026-05-29T20:30:30.092Z","updated_at":"2026-05-29T20:30:30.745Z","avatar_url":"https://github.com/sbalci.png","language":"Groovy","funding_links":[],"categories":[],"sub_categories":[],"readme":"# qupath-extension-workshop\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20375397.svg)](https://doi.org/10.5281/zenodo.20375397)\n[![License: Apache-2.0](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0)\n[![Release](https://img.shields.io/github/v/release/sbalci/qupath-extension-workshop)](https://github.com/sbalci/qupath-extension-workshop/releases/latest)\n\nQuPath extension that bundles the workshop scripts of the **Patologlar için QuPath** workshop (Dijital Patoloji \u0026 Yapay Zekâ) as one-click menu entries.\n\n\u003e Modeled after the official [QuPath extension template](https://github.com/qupath/qupath-extension-template).\n\n## Citation\n\nIf you use this software in published work, please cite it using the metadata in [`CITATION.cff`](CITATION.cff). You can cite all versions by using the DOI [`10.5281/zenodo.20375397`](https://doi.org/10.5281/zenodo.20375397) — this DOI represents all versions and will always resolve to the latest one.\n\n## What it does\n\nAfter installation, a new **Extensions → Atölye** submenu appears in QuPath:\n\n```\nExtensions\n└── Atölye\n    ├── — Atölye scriptleri —\n    ├── ─────────────────────\n    ├── Modül 2 - Hücre tespiti\n    ├── Modül 3 - Nükleer boya (Ki-67)\n    ├── Modül 4 - Membranöz boya (HER2)\n    ├── Modül 5 - Sitoplazmik boya (CD68)\n    ├── Modül 6 - Tümör vs stroma sınıflandırıcı\n    ├── Modül 7 - Tümör içi Ki-67\n    ├── ─────────────────────\n    └── Atölye hakkında…\n```\n\nEach item runs the corresponding workshop Groovy script: friendly Turkish dialogs explain what's about to happen, sensible defaults are applied, and the results pop-up gives measurements plus research/education context.\n\nThe extension is a convenience wrapper around the loose scripts at [handson/scripts/](../handson/scripts/). Both coexist: the loose scripts surface via **Automate → Project scripts** when the workshop project is open; the extension provides the same scripts without requiring participants to open the workshop project.\n\n## Requirements\n\n- **QuPath 0.6.0** or newer (baseline targeted by this build; works up to 0.7.x)\n- Java 17+ (bundled with QuPath; no separate install needed)\n- Module 8 / StarDist / QuANTUM are reserved for later workshop versions and are not required for this release.\n\n## Build\n\n```bash\n./gradlew clean build\n```\n\nOutput: `build/libs/qupath-extension-workshop-0.1.0.jar`\n\n(On Windows: `gradlew.bat clean build`.)\n\n\nIf you don't have the Gradle wrapper checked in, run `gradle wrapper` once or use a globally-installed Gradle 8.x.\n\n## Install\n\n1. Open QuPath (0.6.0+).\n2. Drag the built `.jar` onto the QuPath main window.\n3. QuPath asks: *\"Move to extensions folder?\"* → click **Yes**.\n4. Restart QuPath.\n5. **Extensions → Atölye** menu appears.\n\n## Distribution\n\nThe compiled JAR can be hosted on a GitHub Release. Users install via QuPath's built-in extension manager:\n\n1. **Extensions → Manage extensions**\n2. Add this repo URL: `https://github.com/sbalci/qupath-extension-workshop`\n3. Click Install — QuPath fetches the latest release JAR.\n\n## Versioning\n\n| Version | Date    | QuPath baseline | Notes                                |\n|---------|---------|------------------|--------------------------------------|\n| 0.1.0   | 2026-05 | 0.6.0+           | İlk yayın — 7 modül scripti          |\n\n## How it works internally\n\n- `WorkshopExtension.java` implements `qupath.lib.gui.extensions.QuPathExtension` and is discovered by QuPath via the `META-INF/services/qupath.lib.gui.extensions.QuPathExtension` service loader file.\n- On install, it creates the **Atölye** submenu under **Extensions** and registers one menu item per workshop script.\n- Each menu item, when clicked, reads its script from `src/main/resources/scripts/` (packaged inside the JAR) and evaluates it through a fresh `GroovyShell` on a background thread.\n- The scripts themselves use `qupath.lib.gui.dialogs.Dialogs` for user interaction, so they run identically whether launched from this menu or from `Automate → Project scripts`.\n\n## License\n\nApache 2.0 — matches QuPath itself.\n\n## Disclaimer\n\n⚠️ Yalnızca **araştırma ve eğitim** amaçlıdır. Klinik karar verme için onaylı tıbbi cihaz değildir.\n\n\n\n\n## Local build and install steps\n\n```\n[System.Environment]::SetEnvironmentVariable('JAVA_HOME', 'C:\\Program Files\\Eclipse Adoptium\\jdk-21.0.7.6-hotspot', 'Machine')\n```\n\n\n```\nAdd-Content $PROFILE \"`n# Override broken Machine-scope JAVA_HOME with working JDK 21\n`$env:JAVA_HOME = 'C:\\Program Files\\Eclipse Adoptium\\jdk-21.0.7.6-hotspot'`n\"\n```\n\n```\n$env:JAVA_HOME='C:\\Program Files\\Eclipse Adoptium\\jdk-21.0.7.6-hotspot'; .\\gradlew.bat clean build\n```\n\nThen update tag and push\n\n```\ncd qupath-extension-workshop\ngit tag v0.1.0\ngit push origin v0.1.0\n```\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsbalci%2Fqupath-extension-workshop","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsbalci%2Fqupath-extension-workshop","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsbalci%2Fqupath-extension-workshop/lists"}