Use of fluorescence in situ hybridization and the daime image analysis program for the cultivation-independent quantification of microorganisms in environmental and medical samples. Cold Spring Harb Protoc 2009: pdb prot5253

Conventional cultivation-based methods to measure microbial abundance are unsuitable for quanti-fying uncultured microorganisms that constitute the majority of microbial life in most environmental or medical samples. This problem is solved by the quantification approach described here, which com-bines fluorescence in situ hybridization (FISH) with rRNA-targeted probes and digital image analysis