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This repository contains all the code required to reproduce the image‑based quantification workflow used in this study. The workflow is designed to quantify staining intensity in tissue microarray (TMA) cores by first isolating stained pixels using a calibrated color threshold and then measuring their corresponding grayscale (intensity) values. The pipeline is organized into four sequential stages: Slide acquisition: Stained TMA slides are digitized at high resolution and stored as pyramidal whole‑slide image files to support multiscale processing and visualization. Core localization and extraction: TMA core positions are automatically identified and, where necessary, corrected. Using these coordinates, individual cores are extracted from the whole‑slide image and saved as high‑resolution cropped images for downstream analysis. Quality control: Extracted cores are manually reviewed to identify and exclude samples with visual artifacts (e.g., tissue loss, folding, staining artefacts, or scanning defects) that could bias quantitative measurements. Only cores passing this quality control step are retained. Threshold calibration and quantification: A color threshold is calibrated using a grid‑search approach to optimally distinguish stained pixels, informed by comparisons between tumor and normal tissue samples. The calibrated threshold is then applied uniformly to all retained cores. For each core, grayscale intensity values are quantified over the threshold‑selected pixel population. All intermediate and final outputs—including core position files, cropped core images, threshold parameters, and per‑core intensity measurements—are saved to disk to enable inspection, reuse, and full reproducibility of the analysis.