A bottom read measurement is usually used in cell based experiments when a lid is needed to prevent contamination or when a plate is sealed to prevent evaporation.
Fluorescence calcium signaling (FURA-2, FLUO-3/4/8, Indo, etc.) and
transcription assays (beta-lactamase, GeneBLAzer®, etc.) all need
sensitive bottom reading to be properly executed. In addition, assays dealing with reporter proteins, like GFP/CFP or YFP need bottom reading capability to provide best results.
A bottom read measurement can also be used in kinetic assays that require an injection such as calcium flux or ORAC.
For more information on direct optic bottom reading visit: http://www.bmglabtech.com/technology/bottom-reading.cfm