1. A method for cell-based tissue analysis, comprising: obtaining consecutive tissue sections from a tissue sample, the consecutive tissue sections having consecutive relation associated therewith, mounting each of the tissue sections on one of a plurality of histology slides, and independently staining each of the tissue sections with a histology stain; acquiring a digital image for each of the plurality of histology slides containing the independently stained consecutive tissue sections, wherein a plurality of digital images are obtained for the plurality of corresponding histology slides or portions thereof; associating each of the digital images with its corresponding independently stained consecutive tissue sections in relation to the tissue sample; detecting cells within one or more of the digital images, with the detected cells: measuring one or more cell features of the detected cells with respect to each image and each histology stain associated therewith, said cell features comprising: cell morphology, cell expressions, staining characteristics, cell neighborhood characteristics, cell region characteristics, or a combination thereof, multiplexing the measured cell features across the digital images of adjacent tissue sections to assemble three-dimensional cell-based data, and representing the cell-based data on a computerized display using interactive computer-generated visualizations; identifying cell populations within the three-dimensional cell-based data, said cell populations comprising one or more groups of cells categorized by having the one or more measured cell features representative of said cell populations, and with the identified cell populations: measuring one or more cell population features, categorizing cell subpopulations within the identified cell populations based on the one or more measured cell population features, and representing the cell subpopulations on a computerized display using interactive computer-generated visualizations; and storing information associated with the detected cells, cell features, cell populations, and cell population features in one or more databases for subsequent comparative analysis.