1. A method for the detection of cells with molecular marker compartmentalization associated with malignancy and/or disease including a cancer, the method comprising the steps of: a) obtaining a cell sample having a plurality of cells and suspending the plurality of cells in a solution; b) if required, fixing the plurality of cells of the cell sample; c) labeling at least one molecular marker in the plurality of cells with tagged molecular probes or stains; d) illuminating at least one cell of the plurality of cells with at least one point source of light; e) obtaining at least two different projection images through the at least one cell with a digital array detector; f) compensating the at least two projection images for variations in illumination; g) analyzing the at least two projection images to detect at least one labeled molecular marker having densitometric and location features; h) analyzing the location of the at least one molecular marker within the at least one cell; i) measuring compartmentalization of the at least one labeled molecular marker by using the densitometric and location features; and j) analyzing compartmentalization of the at least one labeled molecular marker with at least one classifier for the detection of malignancy and/or disease associated molecular marker-compartmentalization.