Cell Painting PLUS: An Iterative Staining-Elution Protocol for High-Content Phenotypic Screenings

Cell Painting (CP) methods use a combination of fluorescent dyes to label multiple cellular compartments simultaneously, enabling the comprehensive analysis of phenotypic changes through morphological profiling. Here, we present a detailed protocol for the Cell Painting PLUS (CPP) method along with an automated image and data analysis strategy. In CPP, the iterative staining, elution, and re-staining of cells with seven fluorescent dyes enable multiplexed analysis of nine cellular compartments and organelles. Each dye is captured in individual imaging channels to specifically distinguish effects on the plasma membrane, actin cytoskeleton, cytoplasmic and nucleolar RNA, lysosomes, nuclear DNA, endoplasmic reticulum, mitochondria, and Golgi apparatus. During the image analysis procedure, 894 morphological features (readouts) are extracted from single cells to generate comprehensive phenotypic profiles that resemble morphological perturbations. For efficient processing of the extracted features, we provide an automated data analysis workflow, which includes quality control, data normalization, and various data visualization tools. This workflow is based on a customized CPPAnalyzer Jupyter notebook and a CPPManager KNIME workflow, which can be easily applied without any special bioinformatics knowledge. In this way, CPP expands the multiplexing capacity, customizability, and, importantly, organelle specificity of the available CP-based screening methods. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Seeding of U2OS, MCF-7, or HepG-2 cells in multiwell plates and treatment of cells with compounds Support Protocol 1: Preparation of assay-ready compound plate Alternate Protocol: Seeding and differentiation of primary RPTEC-TERT1 cells in multiwell plates Basic Protocol 2: Staining and imaging of cells using Cell Painting PLUS Basic Protocol 3: Image analysis Basic Protocol 4: Data normalization and data quality control Basic Protocol 5: Visualization of data using CPPManager KNIME workflow.