Abstract: A method of performing an assay to detect and quantify changes in morphology or intracellular events in living or dead cells. The method comprises the step of presenting the cells on a surface for analysis in a single sample or array of samples and providing a means of fluorescently labelling cell structures, engulfed or associated particles or molecules contained on or within the cells. The cells are scanned with a detection system to obtain a linearseries of intensity values at intervals of 10 microns or less across each cell to produce line amplitude data in at least one emission band. A threshold algorithm is applied to determine the beginning and end of each feature on the line amplitude data, whereina feature is any perturbation from a determined background signal.