The methods of enumeration in microbes can be divided into four categories. Direct methods involve counting the microbes, while indirect methods involve estimation. Viable methods only count cells that are metabolically active, while total counts include dead and inactive cells.

A direct/viable method involves a standard plate count, in which repeated dilutions of a sample are counted to calculate the count in the original sample.

Indirect/viable methods such as MPN (most probable number) involve making a statistical inference about the microbe count based on patterns of growth.

The microbes are counted with the aid of fluorescent stains and dyes, which make the microbes visible with the aid of a fluorescent microscope.

Spectroscopy is a form of indirect/total enumeration, which involves estimating the amount of microbes based on the amount of light passed through the culture by a spectrophotometer.