AbstractA method is presented which allows accurate automatic quantification of the protective effect of drugs in cardiomyocytes. Isolated myocytes, obtained by enzymatic digestion of heart tissue by collagenase, are kept in petri dishes which can be mounted on a microscope table. Test compounds are added to the medium. Light intensity settings and focus positions are automatically adjusted, and a number of consecutive images is acquired by scanning the stage with stepper motors, capturing frames, and storing the (pre‐)images on disk. After applying a pathological stimulus to the cells, cardiomyocytes display an irreversible hypercontracture from rod‐ to round‐shaped cells. The same fields (post‐images) are captured again and also stored. After image segmentation and labeling, corresponding cells in the pre‐ and post‐images are measured and classified into ‘rod‐’ and ‘round‐shaped’ groups. Finally, the protection factor is calculated as the percentage of cells remaining rod‐shaped after the stimulus (survival fraction). This value is printed together with a composite image of the selected cells before and after aggression for archiving and quality control. The protection factors are evaluated to select promising cardioprotective drugs. Protection values are incorporated into a database for pharmacological information retrieval, and can be further used for determining structu