Methods and apparatus for evaluating the quality of an environment or process by measuring light emitted from a bioluminescent sample containing ATP, ADP, or alkaline phosphatase. The apparatus comprises a sample collection and analysis system used to collect a sample, mix reagents, react the sample, and collect it in a measurement chamber. The system includes an instrument having a photon detection assembly for use with the sample testing device and one or more probe assemblies that optically cooperate with the instrument. The instrument includes a dark chamber with a reflective interior surface which may be concave or preferably spherical, and a photon detection sensor such as a multi-pixel photon counter sensor. A substantially transparent portion of the probe assembly, and liquid contained therein, focus bioluminescence toward the photon detection sensor.