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Histology: An overview: want to learn more about it?

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Histology: An overview

Eukaryotic cell

Human anatomy is pretty straightforward. If you were to look at some bones on a skeleton, you’d see a greyish rigid mass with some bumps and depressions. However, if you take a much closer look, you’ll see that the histology of bones, is a whole other story. 

Histology is the science of the microscopic structure of cells, tissues and organs. It also helps us understand the relationship between structure and function. By examining a thin slice of bone tissue under a microscope, colorized with special staining techniques, you see that these seemingly simple bones are actually a complex microworld containing an array of structures with various different functions. In this article, we will introduce you to the microscopic world of histology.

Key facts about histology
Histology Microanatomy or microscopic anatomy,
The study of cells and tissues, from their intracellular components to their organization into organs and organ systems.
Cell structure Cellular membrane, cytoplasm, organelles, nucleus
Tissues A unity of cells with a similar structure that as a whole express a definite and unique function.
Epithelial, connective, muscle, nervous
Organs A unity of tissues with a more complex set of functions, defined by the combination of structure and function of the comprising tissues
Systems of organs A group of organs united by similar functions.
Cardiovascular, nervous, integumentary, musculoskeletal, respiratory, digestive, excretory, endocrine, lymphatic, reproductive
Histology techniques Tissue preparation, tissue staining, microscopy, hybridisation

Cells and tissues

A cell is the smallest functional unit of an organism. All cells of the human body are eukaryotic, meaning that they are organized into two parts: nucleus and cytoplasm

The cytoplasm contains specialized subunits called organelles which work like ‘little organs’. Organelles can be membranous (mitochondria, Golgi apparatus, endoplasmic reticulum) or non-membranous (ribosomes, nucleolus, centrioles). 

Thoroughly learn the parts of a cell using our diagrams and cell quizzes! Then, get ready to test your knowledge!

The nucleus is considered to be the brain of the cell. It houses information about each and every structure and process of the cell and organism, in the form of DNA (deoxyribonucleic acid). DNA is condensed and coiled up into chromosomes. All cells are enveloped by a semipermeable two-layered membrane, which serves as a dynamic medium for the cell’s interaction with the external environment. Kind of like border police, it controls everything that comes in or out of the cell. Cells are categorized into various types, all of which perform different functions. These include epithelial cells, fibroblasts, neutrophils, erythrocytes, keratinocytes, chondrocytes just to name a few.

Main tissue types

Cells come together with extracellular matrix (a jelly-like fluid) to form the four types of tissues found in the human body: epithelial, connective, muscle and nervous. Tissues join together in different arrangements to form our body organs. Organs work together in systems.

Epithelial tissue

Epithelial tissue can cover external surfaces (skin), line the inside of hollow organs (intestines) or form glands. It is composed of densely packed epithelial cells with only a little extracellular matrix (ECM). The cells are laid down on top of dense irregular connective tissue, the basement membrane (BM).

Epithelium is classified by both it’s cellular morphology and the number of cell layers. Based on morphology, epithelial cells can be either squamous (flat), cuboid (cube) or columnar (rectangular). Depending on the number of layers, epithelial tissue is classified into simple (single layered) or stratified (multi-layered). Together this gives us the various types of epithelial tissues, such as simple squamous epithelium, stratified cuboidal epithelium, pseudostratified columnar epithelium and many more. Additional sub-classifications are possible, based on the cell specializations.

Get an overview of the different types of epithelial tissue:

Connective tissue

Connective tissue connects, separates and supports the body organs. It consists of a few cells and an abundance of extracellular matrix. The ECM contains different protein fibers (collagen, reticular, elastic) embedded in ground substance. Depending on the type of cells present (fibroblasts, osteocytes, erythrocytes) and the ECM arrangement, connective tissue can be classified as connective tissue proper or specialized connective tissue. Connective tissue proper is further subdivided into loose connective tissue, mostly found in internal organs as supporting tissue stroma, and dense connective tissue, which can be regular (tendons, ligaments) or irregular (dermis of the skin, organ capsules). Specialized connective tissue includes the blood, reticular, cartilage, bone and adipose tissue. A third type of connective tissue is embryonic (fetal) tissue, this is a type of primitive tissue present in the embryo and umbilical cord.

Nervous tissue

Nervous tissue is made of cells (neurons and glial cells) and extracellular matrix. The ECM of nervous tissue is rich in ground substance, with little to no protein fibers. Neurons are specialized cells that contain a body (soma) and one or more processes (dendrites, axons). Based on the number of processes, neurons are classified into multipolar, bipolar and unipolar. Neuronal processes form connections (synapses) with each other and with other cell types, in order to exchange electrical signalsGlial cells, such as astrocytes, oligodendrocytes, Schwann cells and others, provide support, nourishment, myelination and protection to neurons. Supporting cells don’t get as much credit as neurons in popular culture; but did you know that glial cells make up at least 80% of nervous tissue?

Muscle tissue

Muscle tissue maintains synthesizing and contractile functions. It is categorised as skeletal, cardiac or smooth. Based on their functional properties, these are described as either voluntary (skeletal) or involuntary (cardiac and smooth muscle). Despite their differences, they all have one thing in common; specialized elongated muscle cells, called muscle fibers. These cells contain contractile filaments (myofibrils) called actin (thin) and myosin (thick). Under light microscopy, skeletal and cardiac muscles appear striated due to the parallel arrangement of their contractile filaments into repeating units called sarcomeres. Smooth muscle tissue appears non-striated because of the less orderly arrangement of their filaments. Muscle cells have a specialized type of smooth endoplasmic reticulum called sarcoplasmic reticulum, which stores calcium ions. All of these features give muscles the ability to contract and perform various functions, such as movement of the extremities (skeletal muscle), peristalsis of the gastrointestinal tract (smooth muscle) and beating of the heart (cardiac muscle).

Cardiovascular system

The cardiovascular system consists of the heart and blood vessels (arteries, arterioles, capillaries, venules, veins). This system delivers oxygenated blood from the heart to the tissues, and returns deoxygenated blood from the tissues back to the heart and lungs. At a histological level, both the heart and blood vessels consist of three layers: 

  • Endothelial layer - epithelial tissue formed by simple squamous (endothelial) cells. In the heart, this layer is referred to as endocardium.
  • Muscular layer - smooth muscle in the blood vessels, cardiac muscle (myocardium) in the heart.  
  • External layer - loose connective tissue (adventitia) in blood vessels, squamous epithelial (mesothelial) layer in the heart (epicardium). The epicardium is lined by an additional layer of mesothelial cells called pericardium

The myocardium is formed by striated cardiac muscle cells (cardiomyocytes). On a longitudinal section, cardiomyocytes appear branched, joined together by specialized junctions called intercalated discs which allow them to quickly exchange electrical impulses and work as a syncytium. Cardiomyocytes contain actin and myosin filaments just like other muscle cells, but they have some special structural and functional properties. Did you know that there are special cardiomyocytes in your heart that spontaneously generate impulses to initiate heartbeats? How about the fact that some cardiomyocytes have the ability to secrete hormones that regulate blood pressure? 

Nervous system

The nervous system is divided into the central nervous system (CNS) and the peripheral nervous system (PNS). The CNS contains the brain and spinal cord. It is made up of gray matter and white matter. Gray matter is mostly made of neuronal bodies, dendrites and glial cells whereas white matter is made primarily out of myelinated axons. The neuronal bodies within the grey matter are organized into layers (laminae). All of this is surrounded by three connective tissue membranes (meninges): dura, arachnoid and the pia mater.
Epithelial cells form two important histological structures within the brain; the blood-brain barrier and the choroid plexus. The PNS is all neural tissue outside of the CNS, i.e. the peripheral nerves and peripheral ganglia. Peripheral nerves are bundles of myelinated nerve fibers (axons) wrapped in connective tissue (endo-, peri- and epi- neurium). Peripheral nerves are analogous with neural tracts of the CNS. Peripheral ganglia are clusters of nerve cell bodies surrounded by a dense connective tissue capsule. They can be classified as sensory or autonomic.

Integumentary system

The integumentary system consists of the skin and skin appendages. The epidermis (epithelium) and dermis (connective tissue) compose the skin. The epidermis is a keratinized stratified squamous epithelium mostly made out of keratinocytes. The dermis is a layer of connective tissue that contains collagen fibers, blood vessels, lymphatics and nerve endings. Below the dermis, a layer of subcutaneous tissue (hypodermis) is found. It contains connective tissue, mostly composed of adipocytes. Specialised cells (melanocytes, Merkel’s cells, Langerhans cells) and free nerve endings are found within the epidermis, providing pigmentation, protection and sensation. Skin appendages are derivatives of the epidermis. They include hair follicles, skin glands and nails. Hair follicles are invaginations of the epidermis that contain rapidly proliferating and keratinizing cells responsible for the production and growth of hair. Skin glands include sweat glands (apocrine and eccrine) and sebaceous holocrine glands, both are important in regulating body temperature. Nails are plates of proliferating keratinized cells that, similar to hair, contain hard keratin. The skin is both a medium for interaction with the environment and a barrier, protecting us from outside microbes and chemicals, changes in temperature and dehydration. Did you know that the only thing preventing all the water in your body from leaking out through your skin are the tight junctions between the keratinocytes? This is the reason why people with extensive burns are in life-threatening danger.

Musculoskeletal system

The musculoskeletal system consists of hard tissues (bones, joints, cartilage) and soft tissues (muscles, tendons, ligaments). Bone tissue is a specialized type of connective tissue that contains cells (osteoblasts, osteocytes, osteoclasts), fibers (collagen type I) and mineralized extracellular matrix. Bones articulate with other bones by way of joints, which can be synovial, fibrous or cartilaginous. They are stabilized by ligaments, flexible fibrous bands made of dense regular connective tissue. The only freely mobile joints are synovial joints, in which adjacent joint surfaces are covered with hyaline cartilage, a soft type of cartilage rich in glycoproteins, proteoglycans and type II collagen. Skeletal muscle consists of long cylindrical-shaped muscle cells with multiple, peripherally located nuclei and a cytoplasm filled with myofibrils. Multiple muscle cells are bound by connective tissue into fascicles, and multiple fascicles join to form a muscle belly. Muscle attaches to bone via tendons; bundles of dense regular connective tissue made out of many collagen type I fibers. All of these components work together to provide movement to the body. As a muscle contracts, its tendon transmits the force to the bone, pulling on it and causing movement in the associated synovial joint.

Respiratory system

The respiratory system consists of the lungs and a series of passageways (nasal cavities, paranasal sinuses, larynx, trachea and bronchi) that connect alveoli to the external environment. 

Most of the respiratory tract is lined by respiratory mucosa; a pseudostratified columnar ciliated epithelium with mucus producing goblet cells. This traps and removes any inhaled dust, bacteria or foregn substances. The nasal cavity contains specialized olfactory epithelium, providing the sense of smell. Vocal cords are housed in the larynx, formed by two folds of mucosa, each containing a supporting ligament (vocalis ligament) and a skeletal muscle (vocalis muscle). These vibrate to produce sound as air passes through them.

Alveoli are the primary site of gas exchange. Pulmonary capillaries come into close contact with the alveoli, forming the blood-air barrier. The layers of the blood-air barrier comprise of type I pneumocytes, basement membrane and endothelial cells of the capillaries. It is permeable to oxygen, carbon dioxide and other gases, allowing for the occurrence of gas exchange. Type II pneumocytes are also important because they secrete surfactant which prevents the lungs from collapsing. The entirety of the lungs is externally lined by pleura, a thin epithelial layer made of squamous cells with a thin underlying layer of connective tissue.Learn more about the upper respiratory tract and the lower respiratory tract.

Digestive system

The digestive system consists of the alimentary canal and its associated organs (tongue, teeth, salivary glands, pancreas, liver and gallbladder). The alimentary canal is a tube extending from the mouth to the anus that serves as a channel for food and water to be digested, their nutrients absorbed and indigestible portions excreted. It consists of the mouth, pharynx, esophagus, stomach, small intestine, large intestine and anus.

Each organ of the digestive system has properties that make it specialized for its role in the digestion, absorption and excretion of food. For example, the simple columnar epithelium of the stomach fundus contains special parietal cells which secrete HCl to break down meat proteins. Pancreatic serous acini secrete digestive enzymes which break down fat, carbohydrates and proteins. Everything absorbed through the alimentary tract passes through the special discontinued capillaries of the liver before going anywhere else. This is because the liver, among many other things, is the major detoxifying machine of the body. Did you know that chronic alcoholics have a lot more smooth endoplasmic reticulum concentrations in their hepatocytes? This is why doctors must take extra caution when prescribing medication to these people. Learn more about the histology of the upper and lower digestive tract.

Excretory system

The excretory system includes the kidneys, ureters, urinary bladder and urethra. The kidneys clear waste products and control plasma pH, electrolytes and extracellular fluid volume. Thus are essential for maintaining homeostasis of the body. The basic functional unit of the kidney is the nephron. At a microscopic level, a nephron consists of a renal corpuscle and a series of tubules.
The renal corpuscle contains the glomerulus, a tuft of fenestrated capillaries which creates an ultrafiltrate of blood. The glomerulus contains some interesting cells, such as mesangial cells which have supportive and phagocytic properties; juxtaglomerular cells that secrete renin which acts, in a broad sense, to help regulate our blood pressure; podocytes that control the permeability of the filtration membrane; and many more. Once urine is formed from the ultrafiltrate, it travels through the excretory pathway of tubes, all of which are lined by transitional epithelium with the exception of some parts of the urethra.

Endocrine system

The endocrine system is a set of tissues that secrete hormones directly into the bloodstream. These hormones regulate a variety of processes, such as metabolism, growth and blood pressure. It has a similar role as the nervous system, working in tandem with it to maintain homeostasis of the body. The endocrine system is divided into major endocrine glands (e.g. thyroid, ovaries, suprarenal) and individual hormone-secreting cells found in many organs of the body (e.g. adipose tissue, gastrointestinal tract, cardiovascular system). The latter constitutes the diffuse neuroendocrine system (DNES). One could say that the masters of the endocrine glands are the hypophysis (pituitary gland) and hypothalamus, since they regulate all other endocrine organs by way of homeostatic feedback mechanism. Histologically, although there are a few exceptions, endocrine cells generally have an epithelial origin.

Lymphatic system

The lymphatic system consists of a network of vessels and lymphoid organs. It is related to both the circulatory system and the immune system. Lymphatic vessels drain lymph (interstitial fluid) from all the extracellular spaces in the body. They return this fluid to the heart, passing it through lymphoid organs. Primary lymphoid organs (bone marrow and thymus) produce lymphocytes (B and T cells) while secondary lymphoid organs (diffuse lymphoid tissues, lymphatic nodules, lymph nodes and spleen) help to rid the body of toxins, waste and other unwanted material. Spleen and lymph node histology shows an encapsulated meshwork of fibres, in which immune system cells sit. Lymph nodes are distributed along lymphatic vessels, filtering lymph as it passes through. The spleen on the other hand, filters blood. Both respond immunologically to foreign material in the fluid passing through. Diffuse lymphoid tissues and lymphatic nodules are non-encapsulated accumulations of lymphoid tissue found in locations such as the alimentary, respiratory and genitourinary tracts. Some well-known lymphatic nodules include; the tonsils, Peyer’s patches and vermiform appendix. Like the spleen and lymph nodes, the immune cells in this tissue can mount an immune response against foreign invading material.

Immune system

The main effector cells of the lymphatic system are the immune system cells.

  • Lymphocytes – T lymphocytes, B lymphocytes, NK cells. 
  • Support cells – Macrophages, monocytes, neutrophils, basophils, eosinophils and others.

T and B lymphocytes are “born and raised” in the thymus and bone marrow, respectively. Upon maturation, they are released into the blood, lymph and into secondary lymphoid organs, where they work alongside immune system support cells to carry out a detailed surveillance of potential threats. When responding to a foreign threat, immune system cells can activate non-specific inflammation or progress to a specific immune response.

Male reproductive system

The male reproductive system consist of the internal genitalia (testes, genital ducts and accessory genital glands) and external genitalia (penis and scrotum). The accessory genital glands include the prostate, seminal vesicles and bulbourethral glands. Together these organs provide the ability of reproduction and sexual intercourse. 

The testes produce male gametes (spermatozoa) via the process of spermatogenesis. They are organized into lobules, with each lobule containing a parenchyma of seminiferous tubules and a connective tissue stroma. Germinal (spermatogenic) epithelium, with spermatogenic cells and nurse (sertoli) cells, forms the convoluted tubules, while small circular interstitial (Leydig) cells are found in the connective tissue between the tubules. Interstitial cells produce testosterone, a hormone that regulates spermatogenesis. Sertoli cells prevent the immune system from attacking and destroying the spermatozoa. Spermatozoa pass from the testis into the epithelial lined epididymis and ductus (vas) deferens via efferent ductules, then into the ejaculatory duct, which merges with the urethra. The cells of the genital ducts and glands produce secretions to support this process. 

Female reproductive system

Much like the male, the female reproductive system is also designed for reproduction and sexual pleasure. It consists of internal genitalia (vagina, uterus, uterine tubes, ovaries) and external genitalia or vulva (mons pubis, labia majora and minora, clitoris, vestibule, vestibular bulb and glands). The ovary is actually an organ homologous to the male testis, it gives rise to the gametes (ova) and steroid hormones (estrogen, progesterone). When viewing the microscopic anatomy of the ovary, we can see that it consists of a surface germinal epithelium (capsule), ovarian follicles (cortex) and connective tissue (capsule, cortex medulla). The epithelial lining of the uterine tube and uterus play important roles in the transportation and implantation of a fertilized ovum (zygote). There is a lot more to know about the female reproductive system. Continue your learning with these resources.

Fetal tissues

Fetal tissues are classified into two types: mesenchyme and mucoid (mucous) connective tissue. Mesenchyme gives rise to all types of connective tissue. It consists of small, spindle-shaped mesenchymal cells and ground substance with sparse collagen and reticular fibers. Mesenchymal cells are undifferentiated cells, which means they are capable of differentiating into any type of connective tissue cells (fibroblasts, osteoblasts, adipocytes etc.)Mucoid connective tissue is a fetal tissue present in the umbilical cord. It consists of widely separated mesenchymal cells and ground substance with an abundance of hyaluronic acid. This ground substance, also referred to as Wharthon’s jelly, provides insulation and protection to the blood vessels of the umbilical cord.


The tools for studying histology are becoming more diverse everyday. The most used tool today for examining cells, tissues and organs is optic (light) microscopy. For an even more detailed view, an electron microscopy can be used. Other methods include histochemistry, immunocytochemistry, hybridization techniques, tissue culture and many others.

Tissue preparation

The first step in tissue preparation for optic microscopy is fixation. Here, the tissue of interest is immersed in a fixative solution. This preserves it into the same state that it had when it was in the body, and thus, keeps it from degrading. Next, the tissue is embedded with paraffin wax, which firms the tissue enough permit thin slices. The tissue is sectioned thinly enough so that light can pass through it. These sections are then mounted on a glass slide, using a mounting medium as an adhesive. 

Tissue staining

After preparation, the tissue is stained. Since tissues are normally colourless, applying a dye to the tissue section allows the cells and their components to be seen under a microscope. The most common technique used is the hematoxylin and eosin (H&E) stain. Other staining techniques such as Masson trichrome, alcian blue, reticulin stain and others are sometimes used to demonstrate specific tissue components not seen on a H&E stain. Lastly, the specimen is stained with hematoxylin and eosin dyes. Do you know why some structures stain blue (basophilic) and others pink (eosinophilic)? 


Optic microscope

Optic microscopy, also known as light microscopy, uses light from the visible spectrum and combines it with multiple lenses to create a magnified image. The product is the magnifying power of the objective (4x, 10x, 20x, 40x or 100x) multiplied by the power of the ocular lenses (10x). Since tissues are relatively colorless, the magnifying properties of the optic microscope are not sufficient for proper visualization of a specimen; therefore staining techniques described above are coupled with optic microscopy.

Let histology be a piece of cake once you learn how to examine a histology slide!

Electron microscope

Electron microscopy (EM) is a more modern form of microscopy that provides a much higher magnification and high resolution images. EM works by emitting parallel beams of electrons onto the tissue sample. There are two types of EM: transmission electron microscopy, which requires very thin sections of tissue, and scanning electron microscopy, which uses larger pieces of tissue and produces 3-dimensional images. 

In situ hybridisation

In situ hybridisation is a method of localizing and quantifying DNA or RNA sequences. This is done by the use of a complementary nucleotide probe, which contains a radioactive or fluorescent label. This method is based on the ability of single stranded DNA or RNA to merge with a complementary strand and build a hybrid which is then detected due to the label. This technique is used for determining the location of specific DNA or RNA sequences in cells or chromosomes, making it useful for various research and diagnostic purposes.

Blotting technique

Blotting technique is a method of localizing and quantifying proteins, DNA and RNA. One commonly used technique is Western blot, in which proteins are separated from one another based on molecular weight using gel electrophoresis. The proteins are then exposed to labeled artificial antibodies that bind to the protein of interest and catalyse a chemiluminescent reaction, in which light is emitted as a result of a chemical reaction allowing visualization of the protein. Other blotting techniques include Southern blot, Western blot, Far-Western blot, Southwestern blot, Eastern blot, Far-Eastern blot, Northern blot, Reverse Northern blot and Dot blot. 

Histology: An overview: want to learn more about it?

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