Abstract: A system and method for determining the effectiveness of an anaerobic digestion process. The system includes a particle imaging system capable of capturing images of particles, including anaerobic microorganisms, in a fluid and counting those images. The method includes use of the captured image information to relate acquired microorganism information to anaerobic digestion process conditions. The information is further used in the method to adjust the digestion process as may be needed. This allows for an inexpensive means of confirming the bio-assay of an anaerobic sludge and the results of various performance strategies of anaerobic digestion, and may be correlated to a reliable methane output. After verification of the assay genetically, and images correlated to their genetic material, various biological experiments can be performed with exponential reductions in program and laboratory expenditures.