Brain structure is described in three ways.

First is its gross anatomy, its large characteristics that are visible to the eye.

Second is its cellular structure, visible with the help of a classic light microscope.

Third is its dynamic cellular movement, captured by computerized systems that convert fluorescent signals from the brain into images and videos.

Brain’s Gross Anatomy

Brains are very soft, gel-like structures. To protect their fragile makeup, brains are enclosed within a bony case, the skull. The only part of the brain not under bone is the eyes. Unlike other sensory organs that send their signals to the brain via their neuron axons, the eyes are actually brain tissue.

Preserved Human Brain, Pete Spiro,

The term gross anatomy refers to the external features of an organ that can be observed visually and by feel.

The gross organization of the brain is similar among mammalian species. There are two large pieces called the right and left hemispheres.

The hemispheres are connected to each other by a bridge of neuron axons named the corpus callosum.

Within this axon bridge, information travels in both directions functionally connecting the hemispheres.

Corpus callosum comes from two Latin words with corpus referring to a body of tissue and callosum indicating its hard texture, much like the consistency of a callus.

The axons of the corpus callosum connect corresponding parts of the hemispheres and permit the right and left hemisphere to coordinate their activity.

The surface of the brain hemispheres is deeply folded tissue. The top of a ridge is named gyrus and the trough is named sulcus.  Gyrus is a Latin word meaning a circular or spiral form. Whereas, sulcus is a derivative of the Latin word sulcätus, which means to furrow.

There are two additional large structures behind the hemispheres named the right and left cerebellum. The cerebellum is connected to the brain hemispheres by a small structure named the pons.  In Latin the word pons means bridge and cerebellum is a diminutive form of cerebrum, the Latin word for brain. Put together the name of this part of the brain, the part that coordinates complex movement, posture and balance translates into little brain.

Brain Cell Structure

Because of the brain’s soft gel-like appearance, it was considered an irrelevant organ for millennia. Even through the first half of the 1800s scientists claimed that brain was the only organ without cells.

Normal histology stains used at the time to distinguish cellular structure of other tissue did not work in the brain, because the chemicals were widely absorbed by fatty material distributed throughout the brain.

Silver stained brain neuron

Pyramidal neuron of human hippocampus 40X, MethoxyRoxy, Wikimedia Commons

In 1873, Camillo Golgi developed a silver process capable of staining brain neurons. It turned out that Golgi’s silver stain is only taken up by a small percentage, 1% to 3%, of neurons in a tissue slice.

This is fortunate however because a stain that marks all of the neurons would obscure their structure.  With an estimated 86 billion neurons and about 10 times as many partnering cells plus 15-25 square meters of blood vessels, space in the brain is limited.

Santiago Ramón y Cajal and Camillo Golgi shared the 1906 Nobel Prize for their extensive body of work describing the function of brain neurons. Santiago Ramón y Cajal proposed neurons may be separate entities that communicate with each other across narrow spaces. Other scientists, including Camillo Golgi, did not embrace the idea at first. But, Santiago Ramón y Cajal was correct.

Drawing of Cerebellar Neurons

Drawing of Neurons of Chick Cerebellum, Ramon y Cajal

The structures at the places where neurons connect with each other are collectively called synapses.Synapse derives from a Greek work describing a point of contact.

Brain synapses occur at multiple places on neurons, at dendrites, cell bodies, axons and axon terminals.

The complex placement of neuron synapses in the brain permits fine-tuned regulatory control of neuron input and output and creates complex neuronal circuits that act as units.

Animated Neurons

Photomicrograph of a cortical pyramidal neuron

Cortical pyramidal cell capture by con-focal microscopy. Photomicrograph from Lee WCA Plos Biol 4(2):E29 (2006)

A method of microscopy developed since 1990 allows scientists to study living brains. This procedure employs instruments known as optical imaging systems.

This is an invasive procedure restricted to use in animal studies. It requires introduction of genes to fertilized ova to produce fluorescing molecules in the neurons of the brain. It also requires thinning of the bone of the skull, or skull removal over the area of interest.

Fluorescence induced by optical imaging systems in brain tissue is too low to be detected by the human eye.

The con-focal and 2-photon imaging microscopes that detect brain fluorescence are not microscopes in the same sense as traditional light microscopes. Instead, fluorescent light information is analyzed by the computerized optical imaging devices and a computer-created picture displays the information in a form the human eye can recognize.

Computerized microscopic techniques not only permit observation of brain anatomy in greater detail but also display the animated nature of brain tissue. Videos showing neuron animation captured with optical imaging systems are available on YouTube. Two of these are Actin in Dendritic Spines by Michael J Shell and

Neuron Time Lapse Video by Leigh Needleman


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Margaret Thompson Reece PhD is an educator, scientist and author whose expertise lies in the area of human physiology. She  is author of “Inside the Closed World of the Brain–How brain cells connect, share and disengage–and why this holds the key to Alzheimer’s disease.”

book coverDr. Reece served 18 years as a Laboratory Director in academic clinical departments in New York and Massachusetts. Subsequently, until 2012, she served as Chief Scientific Officer for Serometrix LLC, a biotechnology company in Upstate New York discovering new lead compounds for drug development.

Dr. Reece is presently CEO of Reece Biomedical Consulting LLC, a company dedicated to supporting undergraduate life science and graduate medical students in their efforts to master the complexities of human physiology. You may contact Dr. Reece at, +1315-679-6077,  or on LinkedIn.