The study of microorganisms and their ability to cause disease is of great interest to the health care community. The ImageStream's array of image-based features enables classification of bacteria based on their morphology and can be used to identify cells undergoing replication. Pathogenic bacteria have evolved strategies to overcome the immune system, including inhibition of internalization by phagocytes Furthermore, the complex biology of microorganism-host cell interactions can be studied using the ImageStream, including phagocytic uptake and clearance by cells of the innate immune system, persistence and proliferation of intracellular bacteria, and the impact of bacterial infection on host cell signaling and survival.

Species of bacteria from culture or from contaminated food supplies can be identified and quantitated by analyzing for fluorescence intensity of species specific FISH probes, size, and shape. Filamentation, either due to defective replication or as a response to evade host innate immunity can be measured.

Here we identify Salmonella in spoiled food using a specific FISH probe. Positive identification of the microorganisms by imaging confirms separates the organisms from debris.