A QuPath 0.6+ extension that bundles the Patologlar için QuPath Atölyesi (QuPath Workshop for Pathologists) Groovy scripts as one-click menu entries under Extensions → Atölye. Workflow modules: cell detection (M2), nuclear IHC scoring (M3 — Ki-67; M3b — ER/PR H-score), membrane IHC scoring (M4 — HER2, with Cellpose primary detector and WatershedCellMembraneDetection automatic fallback), cytoplasmic IHC scoring (M5 — CD68), tumor-vs-stroma classification (M6), tumor-restricted scoring (M7), and measurement export (M9). Utility helpers: orphan detection cleanup, image-type setup (per-slide or project-wide), and threshold re-binning of existing detections without re-running cell detection. The bundled HER2 pipeline implements both a cell-based H-score and a parallel pixel-wise H-score adapted from Sara McArdle's published Groovy script (method: Ram et al., PLoS One 2021). Scope: research and education only — produces numerical measurements (counts, percentages, intensities, H-scores, densities); clinical interpretation is explicitly out of scope. Companion workshop site: atolye.patoloji.dev

Cite all versions using DOI 10.5281/zenodo.20375397 — this DOI represents all versions and always resolves to the latest one. Companion workshop website at https://atolye.patoloji.dev. The extension JAR is also distributed via OSF at https://osf.io/v7mjq alongside the workshop slide set and pixel classifier.