A method and apparatus are provided for aligning optical elements or microbeads, wherein each microbead has an elongated body with a code embedded therein along a longitudinal axis thereof to be read by a
code reading device. The microbeads are aligned with a positioning device so the longitudinal axis of the microbeads is positioned in a fixed orientation relative to the
code reading device. The microbeads are typically cylindrically shaped glass beads between 25 and 250 microns (μm) in
diameter and between 100 and 500 μm long, and have a holographic code embedded in the
central region of the bead, which is used to identify it from the rest of the beads in a batch of beads with many different chemical probes. A
cross reference is used to determine which probe is attached to which bead, thus allowing the researcher to correlate the
chemical content on each bead with the measured
fluorescence signal. Because the code consists of a
diffraction grating typically disposed along an axis, there is a particular alignment required between the incident readout
laser beam and the readout
detector in two of the three rotational axes. The third axis, rotation about the center axis of the cylinder, is azimuthally symmetric and therefore does not require alignment.