Abstract: A system and method is described for permitting the simultaneous automated collection of data with regard to the presence of diseased cells, in particular neo-plastic, dysplastic or cancerous cells, or normal cells at a given site in a section of tissue. This is accomplished according to the following steps. First, IR spectral data are collected simultaneously for each cell or pixel of the tissue. Next, these data are analyzed by identifying the cell types encountered in the sample by comparing them with reference data sets for healthy and diseased cells. Finally, a false color mapping of the distribution of different types of cells in the tissue section is presented that permits assessment of the prevalence of diseased cells.