A method of detecting fluorescence/absorbance/luminescence from 24-well, 48-well, 96-well, 384-well and 1536-well microplates and other sample containers. The sample is pumped into a waveguide. The waveguide efficiently gathers and guides the emission light to the end of the waveguide. The emission light exits the ends of the waveguide and is focused into a detector. To minimize background caused by the excitation light used for fluorescence, the excitation illuminates the waveguides at 90 degrees. To facilitate reuse, the waveguide assembly can be configured to be washed by an appropriate wash solution.