A system for enumeration of cells in fluids by image cytometry is described for assessment of target populations such as leukocyte subsets in different bodily fluids or bacterial contamination in environmental samples, food products and bodily fluids. Briefly, all cells in a biological sample are fluorescently labeled, but only the target cells are also magnetically labeled. A small, permanent magnet is inserted directly into the chamber containing the labeled sample. The magnets are coated with PDMS silicone rubber to provide a smooth and even surface which allows imaging on a single focal plane. The cells are illuminated and the images of the fluorescent light emitted by the target cells are captured by a CCD camera. Image analysis performed with a novel algorithm provides a count of the cells on the surface that can be related to the target cell concentration of the original sample.