A system and method for analyzing a specimen containing particles that can be difficult to differentiate. The system and method determines a first collective count of a selected group of particles in the specimen, treats at least a portion of the specimen to alter a subgroup of the selected group of particles, determines a second collective count of any of the selected group of particles in the treated portion of the specimen, and subtracts the second collective count from the first collective count to determine a differentiation count for the subgroup of particles altered by the treating of the specimen. The system and method is described with the example of determining concentrations of red and white blood cells in a specimen (e.g. spinal fluid), using auto-particle recognition techniques, without attempting to distinguish and count red versus white blood cells co-existing in the same specimen portion.