A method and system for characterizing a cell population including a set of cell subpopulations, the method comprising: at a processing system, receiving image data corresponding to a set of images of the cell population captured at a set of time points; at the processing system, generating an analysis based upon processing the set of images according to: a cell stage classification module configured to automatically identify a cell class of each of the set of cell subpopulations, and a cell graph representation module configured to characterize geometric and spatial features of the set of cell subpopulations; from the analysis, determining a set of parameters characterizing the cell population; and generating an indication of quality of the cell population based upon a comparison between at least one parameter of the set of parameters and a set of reference values.