Abstract: An embodiment of the invention is directed to a portable, modular, microscope mounted, microfluidic flow cytometry system. The system includes a microscope platform having an optical input/output port, imaging optics, and a sample stage; a sample illumination source module that is removably integrated with the optical input/output port; an optics module that is removably integrated with the sample excitation light source module and the optical input/output port; a detector module that is removably integrated with the optics module and the optical input/output port; a fluidic pump module having a fluidic input and a fluidic output, a first removable fluid conduit for connecting a fluid source to the input, and a second removable fluid conduit for connecting the output to an input of a microfluidic flow module; and, a system control and programmable data processing module.