As the oldest application for microscopes, micro-biological assessments are the most traditional task in medical laboratorys. Their aim is to search and find the pathogenic agents in samples taken from patients. Even if bacteria are the typical cause of infection, fungi, viruses and certain parasites and their eggs are only visible through microscopy. Some of the diseases caused by microscopic lifeforms can be extremely lethal. For instance the plaque or Cholera. Gathering reliable intel on the type and relative amount of pathogens is essential for treatment plans of patients.
Then again, not all bacteria or fungi are pathogenic agents. Some are essential for our survival, some exist in dairy products. Analyzing the cultures in yogurt or cheese is part of quality assessment.