QuPath Atölye Eklentisi (QuPath Workshop Extension): Patologlar için tek-tıkla İHK kantifikasyon ve dijital patoloji eğitim araç seti

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