1. A computer-implemented method of quantifying the activity level of a target biomolecule in a sample comprising one or more intact cells, said sample having been treated with a reagent, said reagent comprising a label that can label a cellular structure such that the label can be localized within the cell, and a binding component that binds the target biomolecule, said target biomolecule comprising a first activity level within the cell and a second activity level within the sample: receiving a set of images of the sample, wherein the images within the set comprise individual cells and are taken at a plurality of depths; detecting a first cell in the images of the sample at the plurality of depths; detecting and localizing the label at individual sites in the first cell at each depth in the plurality of depths; calculating a total number of detected and localized labels within the first cell; and calculating a first activity level of the target biomolecule within the cell based on the total number of detected and localized labels at individual sites in the cell; calculating the first activity level of the target biomolecule within a plurality of cells in the sample; and calculating the activity level of the target biomolecule within the sample based on the number of detected and localized labels in the plurality of cells.