Abstract

Abstract Image‐based cytometry faces challenges due to technical variations arising from different experimental batches and conditions, such as differences in instrument configurations or image acquisition protocols, impeding genuine biological interpretation of cell morphology. Existing solutions, often necessitating extensive pre‐existing data knowledge or control samples across batches, have proved limited, especially with complex cell image data. To overcome this, “Cyto‐Morphology Adversarial Distillation” (CytoMAD), a self‐supervised multi‐task learning strategy that distills biologically relevant cellular morphological information from batch variations, is introduced to enable integrated analysis across multiple data batches without complex data assumptions or extensive manual annotation. Unique to CytoMAD is its “morphology distillation”, symbiotically paired with deep‐learning image‐contrast translation—offering additional interpretable insights into label‐free cell morphology. The versatile efficacy of CytoMAD is demonstrated in augmenting the power of biophysical imaging cytometry. It allows integrated label‐free classification of human lung cancer cell types and accurately recapitulates their progressive drug responses, even when trained without the drug concentration information. CytoMAD also allows joint analysis of tumor biophysical cellular heterogeneity, linked to epithelial‐mesenchymal plasticity, that standard fluorescence markers overlook. CytoMAD can substantiate the wide adoption of biophysical cytometry for cost‐effective diagnosis and screening.