We have studied the designs and working principles of conventional light microscopy, fluorescence light microscopy, electron microscopy, and atomic force microscopy. In this lecture, we shall study the various applications of these microscopic methods. We shall see how the images recorded from these methods look like and what information do they provide.

Light microscopy

In the area of biological sciences, microscopy has traditionally been used to study the structures and organization of cells and organelles. Owing to their poor contrast, bright-field and dark-field microscopic methods typically require a specimen that is stained by some dye. Advent of phase contrast significantly improved the contrast and staining may not be necessary for visualizing the specimen. The ultimate idea behind using a microscope is to magnify the specimen and identify the specific features in the specimen. Fluorescence has become a powerful tool to selectively label the molecules and other cellular structures. Light microscopy finds a variety of applications in studying biological systems some of which are:

(i) Specimen identification and quality: The simplest application of microscopy is to observe the given sample to identify the different components in it. A given sample may have different microorganisms with different morphologies and structures. A simple microscopic analysis will allow identifying these components. Viability of cells, and therefore their quality, is ascertained by staining the cells with dyes that distinguish between live and dead cells.

(ii) Cell counting: Counting of cells using a hemocytometer utilizes light microscopy.

(iii) Classification of bacteria: Differential staining of the bacterial cell wall by Gram staining method is the basis of classifying the bacteria into Gram positive and Gram negative. The stained cells can easily be observed in a bright-field microscope allowing their classification.

(iv) Microscopic analysis of body fluids: Microscopic analysis of blood samples is routinely used to determine the blood cell count, to detect the microbial infection, and to identify any changes in the cellular structures.

(v) Fecal analysis of domesticated animals: Domesticated animals are often infected by the protozoan parasites. Coccidia, for example is always present in the intestine of goats. However, if the number of parasites is very large, it can cause problems. Coccidiosis is a big cause for fetal deaths in goats and sheeps. Coccidia can easily be identified and quantitated by analyzing the fecal samples using light microscopy.