1. A method for quantitative assessment of a patient-specific immune system state in tumor tissue and other relevant tissue compartments for evaluating a potential or ongoing treatment, the method comprising: preparing one or more tissue sections and respective histologic slides from a tissue sample at least partially containing tumor cells, staining said slides with at least: a first stain for identifying cells within the tissue sections, and a second stain for identifying inflammatory cells, inflammatory modulators, or a combination thereof; obtaining digital images of the stained slides; for each of said digital images: detecting cells within the digital image; extracting cell features, cell population features, or a combination thereof to assemble cell-based data, representing the cell-based data with interactive computer-generated visualization; dividing the detected cells into one or more tissue compartments based on the extracted cell data; selecting one of the tissue compartments for further analysis; and within the selected tissue compartment, identifying inflammatory cells, cells expressing an inflammatory modulator marker, or a combination thereof to assemble tissue compartment data; the method further comprising: storing the cell-based data and tissue compartment data in one or more databases for comparative analysis; deriving an immune system state score based on analysis of the cell-based data and tissue compartment data; using at least the immune system state score to stratify a patient into one or more treatment stratification groups; and selecting a particular therapy, treatment efficacy or treatment toxicity level for the patient based on the treatment stratification group.