An Integrated and Configurable End-to-End Pipeline for Longitudinal Cell Painting Analysis

ABSTRACT Cell painting assays generate high-dimensional, multi-channel imaging data that enable systematic characterization of cellular phenotypes. Increasingly, such assays are performed in longitudinal settings and under chronic perturbations, introducing additional challenges related to imaging variability, focus-field heterogeneity, and consistency across time points. Existing analysis workflows often require substantial manual adaptation to handle these complexities, limiting scalability and reproducibility. In this paper, we propose SCALE (Stable Cell painting Analysis for Longitudinal Experiments), an integrated, end-to-end analysis pipeline designed for robust longitudinal analysis of cell painting data. The pipeline combines nucleus-centered segmentation, automated quality control, feature extraction, and signal aggregation within a modular and configurable framework. Once assay-specific configurations are specified, the pipeline executes in a fully automated manner from raw images to downstream summary statistics and analysis-ready outputs. We demonstrate the utility of the pipeline using a chronic radiation exposure cell painting dataset, illustrating its ability to support consistent longitudinal comparisons across conditions and time points.