What is meant by Microscopic Examination?

The analysis of minute organisms, cellular organization of any biological structure, and composition of body fluids with the help of a microscope is known as microscopic examination. The magnification of specimens or samples under study helps in attaining a clearer picture of it.

Why is Microscopy considered a boon?

The field of microscopy refers to the application of microscopes in scientific study. Due to its magnification potentials, microscopes allow better visualization of microscopic (minute) substances. In turn, it provides clear knowledge regarding the structural and cellular organization of different organisms. Therefore, microscopy is considered a boon to science.

Applications of Microscopic Examination

Microscopic examination can be used for the following purposes:

  • Structural analysis of unicellular organisms: The organisms belonging to the kingdom bacteria, protist, archaea, and other unicellular organisms are observed under the microscope. These are minute organisms, and their details are learned only through microscopes.
  • For understanding the cellular level organization of different body structures: The complex organs of multicellular organisms are studied by placing a thin layer of their tissues or cells under a microscope.
  • For detecting the cause of diseases: Certain diseases can be detected by observing the pathogens or pathogenic particles in the diseased body cell under the microscope.
  • Analyzing the content of body fluids: The concentration of body fluids varies under different conditions. The cellular content of body fluids under various conditions can be analyzed and studied for understanding physiological mechanisms.
  • Observation of abnormalities in cell structure or content: The microscopic examination helps to detect the variation in the shape of a body cell or change in its cellular content.

Steps for Microscopic Examination

The sample is prepared under the most suitable method (squash, whole-mount, sectioning, or smear). The specimen sample is then placed over a microscopic slide. Staining chemicals or other liquids are added to the sample, and then it is covered with a coverslip. The slide, after preparation, is placed under the microscope for examination.

The preparation of a sample slide is shown in the image. In the first step, a section is taken from the sample. In the second step, the sample is being stained with a staining agent, for example, methylene blue. In the third step, a coverslip is being placed over the stained sample.
Preparation of sample slide
A prepared sample slide is placed on the microscope for examination, and the magnified image is observed. The magnified view of the sample displays clustered structures that are stained in red color.
Observation of sample slide

Microscopic examination for laboratory purposes

Examination with the help of microscopes is an integral part of laboratory studies. Microscopic examination is used for detecting the presence of pathogens and in checking the severity of a disease. Microscopic analysis in laboratories generally involves semen analysis, blood analysis, CSF (cerebrospinal fluid) analysis, and urine analysis. Among these, urine analysis is the most common. The test results of these examinations suggest the health condition of an individual.

Semen analysis

Microscopic analysis of semen helps in evaluating the fertility level of men. It examines the count of motile sperms and the liquid part, referred to as the seminal fluid. It also helps in observing the abnormality in the shape, structure, and motility of the sperms.

Blood analysis

Blood is the special fluid of the body that serves multiple functions. Blood transports essential nutrients, hormones, and oxygen to body cells. Laboratory microscopic analysis of blood is only helpful in counting the blood cells, visualizing the change in their number, shape, and color.

Cerebrospinal fluid (CSF) analysis

The microscopic examination of CSF is done to detect diseases or disorders of the brain. The fluid is examined for counts of erythrocytes and leukocytes. Detection of erythrocyte indicates blood leakage, and the presence of more than normal leukocytes suggests infection. The fluid is analyzed for the detection of brain and spine damages.

Microscopic urinalysis

The microscopic examination gives a clearer image of the abnormalities found in the urine sample and helps understand the underlying cause of the condition. The examination is done with urine sediments (the bottom portion of the urine sample after centrifugation). The test results of cells or crystals are counted and denoted in terms of the microscopic power used for examination. The count can be represented as per LPF (Low Power Field) or HPF (High Power Field). The value of some substances is denoted by terms like few, many, or moderate.

Red blood cells (RBCs) count

A urine sample in normal health conditions will have an RBC count ranging between zero to five RBCs per HPF (High Power Field). The presence of red blood cells or hemoglobin in the urine indicates various abnormalities. Though the source of blood cannot be predicted, this test result suggests kidney disease or urinary tract infection.

Count of white blood cells (WBCs)

Typically, the urine examination of a healthy individual will have very low counts of white blood cells (also termed leukocytes), approximately 0 to 5 WBCs per HPF (High Power Field). A higher count is indicative of inflammations in some parts of the urinary tract. Women should be extra careful while providing urine samples, as contamination from vaginal secretions may alter the result for leukocytes.

Levels of epithelial cells

The observation for the presence of epithelial cells is done under the low power resolution of the microscope and the result is indicated as few, many, or moderate. Under normal conditions, the levels of these cells in the test sample are few (both for men and women). A urinalysis report with 'many' epithelial cells indicates complications in some regions of the urinary system; this can be detected by identifying the type of epithelium found during the analysis.


The urinary system of healthy individuals remains free of microbes, and a clean-patch sample collected from healthy individuals will have zero detection of microbes. Microbes presence is reported with terms such as few, many, or moderate. The presence of bacterial colonies indicates contamination from nearby regions, which may enter the urinary tract via the urethra; if the treatment is delayed, it may infect the kidneys and causes pyelonephritis. Trichomonas vaginalis is a parasitic microorganism, which generally infects the vagina. During urine sample collection in females, these microbe flows into the sample and are detected during the testing procedure. The presence of Trichomonas vaginalis is further confirmed using Trichomonas testing.


Under normal conditions, a count of approximately five casts per LPF (Low Power Field) is observed during testing. The coagulation of kidney proteins forms the cast. It takes the shape of the region of its formation. Casts with trapped blood cells, fatty substances, or some other material indicate kidney disease. The analysis of these unusual casts helps in identifying the type of diseases associated with the kidney.


The solutes eliminated by the body are excreted via the urine and are usually in a dissolved state. If the concentration of the solutes increases above the normal range, or there is variation in the urine pH (turns extremely basic or acidic), the dissolved solutes may form crystalline structures. At the time, the temperature of the urine also facilitates crystal formation. Crystals of solutes that are normally absent in urine indicate health issues. In certain cases, medicinal compounds, drugs, or X-ray dyes can also form crystals in the urine.

The upper half of the image displays two unusual types of crystals (cholesterol and leucine) that can be observed during urinalysis. The lower half shows two types of casts (granular and WBC cast) that can be detected in urinalysis examination.
An example of casts and crystals observed during microscopic urinalysis

Common Mistakes

The technique of microscopic examination needs to be done very carefully. There is a misconception that there is a generalized method for microscopic examination. Each specimen requires a particular method for slide preparation and magnification power for accurate examination.

Context and Applications

This topic is significant in the professional exams for both undergraduate and graduate courses, such as

  • Bachelor of Science in Biology
  • Bachelor of Science in Microbiology
  • Bachelor of Science in Nursing
  • Master of Science in Nursing
  • Master of Science in Microbiology

Relatable Concepts

  • Laboratory Testing
  • Research Studies
  • Microbial Study

Practice Problems

Q1: Which of the following is not an application of microscopic examination?

(a) Detection of the structural composition of a tissue.

(b)Treatment of diseases

(c) Microbial growth

(d) Both (b) and (c)

Correct choice: (d)

Q2: Microscopic analysis for laboratory testing involves the study of?

(a) Semen

(b) Cell division

(c) Vascular tissues

(d) Chromosomes

Correct choice: (a)

Q3: Blood analysis through microscope helps in estimating the levels of?

(a) Glucose concentration

(b) Hormonal levels

(c) Blood cell count

(d) All of the above

Correct choice: (d)

Q4: During urine analysis which component is observed under high power?

(a) Microbes

(b) Red blood cells

(c) Epithelial cells

(d) Casts

Correct choice: (b)

Q5: What are some of the methods for preparing a microscopic slide?

(a) Whole-mount

(b) Squash

(c) Both (b) and (c)

(d) Cutting.

Correct choice: (c)

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