There are several methods to detect analytes in the microscale. These vary from characterizing some specific property of the analyte being measured. One interesting method that has been used by Dr Richard Wilson of University of Houston is to create retroreflectors that are bound to specific antibodies or ligands. Retroreflectors normally reflect all the light back to the source but in case the ligand is occupied then the light cannot be reflected back. This extremely simple principle when used in the nano scale enables detection in the Microfluidic chambers as well facilitates the detection of several different analytes. The need to compact several of these detectors in a small space would enable the detection of several different entities. Dr Wilson’s interest is in the detection of pathogens and in that area, rapid and quick detection of several pathogens would make a big difference to the industry – hopefully, the formation of the tricorder: Star Trek / Star Wars detection of disease through a hand held device that scans the person.
Interestingly, retroreflectors are an interesting physics phenomenon wherein all the light from source is turned 180 degrees and sent back to the source. These are commonly used in reflectors used in bicycles, or street signs. See this link for their use after lunar landings.