HCS-proc: data processing pipeline for High-Content Screening using CellProfiler data

HCS-proc is the image analysis and data processing pipeline behind a high-content screen of RTgill-W1 fish gill cells exposed to Tebuthiuron, published in Tome et al. 2026. It runs from raw microscopy images to the reduced feature space the article's conclusions rest on: image-level quality control by CellProfiler-Analyst classifiers, CellProfiler feature extraction, per-cell pooling, row and plate standardization with percentile trimming, concentration-response feature selection by earth mover's distance (EMD) and multi-model curve fitting, feature categorization, and dimensionality reduction by UMAP alongside MMD, EMD and Mahalanobis distance measures. Each step is a script driven by an .ini configuration file, and the README documents the sequence they must run in. Release v1 (10.5281/zenodo.17949848) is the exact code used for the article; later releases carry corrections and extensions. The concentration-response feature selection has since been generalised into the standalone tool cdr_FS (10.5281/zenodo.22047439).