1. A method for cell-based tissue analysis, comprising: preparing one or more tissue sections and respective histology slides from one or more tissue samples using stains, staining processes and controls that are optimized for use with image analysis; creating calibrated digital images of the histology slides using the controls and stain-specific color calibration targets; detecting cells within the digital images, with the detected cells: measuring and calibrating one or more cell features and multiplexing cell features across adjacent tissue sections to assemble cell-based data, and representing the cell-based data with interactive computer-generated visualizations; identifying cell populations using the cell-based data, with the identified cell populations: calculating and calibrating one or more cell population features, interpreting cell populations, and representing the cell populations with interactive computer-generated visualizations; and storing information associated with the tissue samples in one or more databases for comparative analysis.