HBTRC Neuroanatomy 2014.1 PDF

An Introduction To
Human Neuroanatomy
Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, MA 02478, 1-800-BRAIN BANK.
Created by Tim Wheelock, Assistant Director of Neuropathology/Instructor in Neuroanatomy
Welcome
This Introduction to Human Neuroanatomy provides a look at the structure of the human brain. In
it, we will explore each major region of the brain, as well as the brain’s coverings, blood supply,
and ventricular system. We hope that this presentation proves interesting and informative.
Please feel free to relay any questions, comments, or suggestions you may have. Thank you.
Subjects and brain regions covered in this presentation
• The brain’s surfaces

• Directional terminology and planes of section
• The divisions of the brain
• The meninges: the brain’s coverings
• The cerebral cortex
• Neurons and glia (support cells)
• The brain’s blood supply
• The ventricular system and cerebrospinal fluid.
• The hippocampus
• The amygdala
• The striatum
• The thalamus
• The hypothalamus
• The cerebellum
• The brainstem
Dorsal view of a human brain
Anterior
Lateral Lateral
Credit: Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, MA. 1-800-BRAIN BANK
Posterior
Ventral view of a human brain
Anterior
Lateral Lateral
Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, MA.
Posterior
Medial view of a left half brain
Dorsal
Anterior
Posterior
Ventral
Lateral view of a left half brain
Dorsal
Anterior
Posterior
Ventral
Dorsal
Summary Of Directional Terms
Anterior (rostral)
Lateral
Ventral Posterior (caudal) Medial
Black and white images from: “The Human Brain” by Henri M. Duvernoy, Publisher: Springer-Verlag/Wien; 1999.
Color image: Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, MA. 1-800-BRAIN BANK
Planes of Section
Coronal cut
Sagittal cut
Horizontal cut
Black and white image from: “The Human Brain” by Henri M. Duvernoy, Publisher: Springer-Verlag/Wien; 1999.
Left hand color images from: Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, MA. 1-800-BRAIN BANK
Right hand myelin-stained sections from the Yakovlev-Haleem Collection, Washington, DC
Summary of basic cuts
Horizontal cut
Sagittal cut
Coronal cut
Credit: “The Human Brain” by Henri M. Duvernoy, Publisher: Springer-Verlag/Wien; 1999.

Oblique Cut
Credit: Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, MA.
1-800-BRAIN BANK Credit: Neuroanatomy: Text and Atlas by John H. Martin.
Publisher: Appleton and Lange: 1989
Sometimes, in order to see a structure more clearly, we have to cut the brain at an
off-angle (called an oblique cut). On the left, we have made a cut from the
cerebral cortex down through the brainstem. As a result, on the right, we can see Motor command
the fiber pathways (stained black) that, among other things, carry motor pathway
commands down through the brainstem to the spinal cord.
Dividing up the brain
• As we will see in the following seven pictures, we can divide the brain up in various ways.
• First picture: The two cerebral hemispheres are seen from a dorsal view of the brain.
• Second picture: The cerebrum (forebrain) and brainstem (hindbrain) from a ventral view.
• Third picture: Dividing the whole brain into a half-brain.
• Fourth picture: Dividing the half-brain into a cerebral hemisphere and a (half) brainstem.
• Fifth picture: A cerebral hemisphere.
• Sixth picture: The medial surface of a half-brain is used to divide the brain using informal terms.
• Seventh picture: The brain subdivided using Latin terminology, English terms in parentheses.
1 The Two Cerebral Hemispheres
Left Right
hemisphere hemisphere
2 Forebrain and Hindbrain
Cerebrum
(forebrain)
Brainstem
(hindbrain)
Credit: Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, MA.
3 From Whole Brain to Half Brain
Left Half brain
4 Cerebral Hemisphere and Brainstem
Cerebral hemisphere
(forebrain)
Brainstem
(hindbrain)
5 Cerebral Hemisphere
A cerebral hemisphere is a half brain with the brainstem removed

The Brain’s Informal Divisions
6
Cerebral hemisphere
Cerebellum
Medulla
Pons Midbrain
The Brain’s Formal Divisions
7
Telencephalon (end-brain)
Myelencephalon
(medulla) Metencephalon Mesencephalon Diencephalon
(after-brain) (midbrain) (inter-brain)
The Brain’s Formal Divisions
• Encephalon (brain)
– Prosencephalon (forebrain) (cerebrum)
• Telencephalon (endbrain)
– Cerebral hemispheres
» cerebral cortex, white matter, basal ganglia)
» Contain lateral ventricles
• Diencephalon (inter-brain)
– Thalamus, hypothalamus
– Contains third ventricle
– Rhombencephalon (hindbrain) (brainstem)
• Mesencephalon (midbrain)
– Substantia Nigra; cerebral peduncle
– Contains cerebral aqueduct
• Metencephalon (after-brain)
– Pons and cerebellum
– Contains fourth ventricle
• Myelencephalon (medulla)
– Medulla oblongata
– Contains fourth ventricle
This way of dividing the brain uses Latin terminology with the English names in parentheses.
The brain is divided into 2 major divisions and 5 sub-divisions.
Each subdivision contains specific structures that we will explore later.
Each subdivision contains part of the ventricular system where cerebrospinal fluid is created and flows.
The Brain’s Protective Coverings: The Meninges
• The Dura Mater ( Latin for “Tough mother”, as in durable)

– Outermost very tough covering
– Contains the venous sinuses
• The Arachnoid layer (Spider-like layer)

– Middle, thinner layer
• The Sub-arachnoid space

– Contains cerebro-spinal fluid and blood vessels
• The Pia Mater (Latin for “Tender mother”)

– Inner-most delicate covering
– Follows the contours of the brain closely
The Dura Mater
Image credit:http://www.profelis.org/vorlesungen/neuroanatomy_1ns.html: 2013

The Dura Mater and its Venous Sinuses
Credit: Carpenter’s Human Neuroanatomy, Ninth Edition by Andre Parent. Williams and Wilkins, Publisher: 1996
The Dura Mater contains the venous sinuses. These are spaces which receive venous blood
from the veins draining the brain, and which pass the blood on to the internal jugular veins.
The Arachnoid Layer
Beneath the Dura Mater lies the Arachnoid Layer, the translucent milky membrane through which one can
see the cerebral cortex. Beneath the Arachnoid Layer lies the sub-arachnoid space, which contains
cerebro-spinal fluid and the blood vessels lying on the surface of the cerebral cortex.
Cerebral Hemisphere with Blood Vessels and Pia Mater

Cerebral Hemisphere with Blood Vessels removed

Cross-section through the Meninges
Arachnoid layer Dura Mater
Sub-arachnoid space
Blood vessel
Credit: “The Human Brain”, Fifth Edition by John Nolte, Publisher: Mosby Inc.: 2002
Pia mater Brain tissue

The Cerebral Cortex:
The surface of the cerebrum
Gyrus
Sulcus
Fissure
The Five Cortical Lobes
Grey and White Matter
Grey matter White matter
In the above image of fresh, un-fixed slices of brain, grey matter has a reddish brown color and white
matter is white. Grey matter is composed of nerve cell bodies, their input fibers (dendrites) and output
fibers (axons). White matter is composed of those axons that get coated with a protein called myelin that,
in fresh brain, has a glistening white appearance. Grey matter is not confined to the cerebral cortex, as in
the above slices, but can be found in many deeper structures of the brain as well. Sometimes, grey and
white matter are mixed together, as in the Reticular Formation of the brainstem.
Grey and White Matter
Grey matter
White matter
In this stained section of cerebral cortex, the white matter (specifically the myelin protein that coats the
nerve cell axons) has been stained blue with a dye called Luxol Fast Blue. The grey matter has been
stained red with a dye called Eosin.
Luxol Fast Blue-Hematoxylin-Eosin stain
Cells of the Cerebral Cortex
• Neurons (nerve cells)

– Principle neurons
• Nerve cells that communicate with other neurons by exciting them.
– Interneurons
• Inhibitory nerve cells that control principle neurons and other interneurons.
– Cajal-Retzius cells
• Nerve cells that guide other neurons during development of the cortex.
• Neuroglia (cells that support the neurons)
– Astrocytes
• controls communication between neurons at synapses.
• coats neurons and capillaries to influence metabolism.
• produces glial limiting membrane that covers the brain.
• producing scaffolding that guides cortical development.
– Oligodendrocytes
• make myelin protein that insulates nerve cell axons
– Microglia
• immune system surveillance cells
• Endothelia
– cells that line the inner wall of blood vessels
The Neuron
Cell Body (soma)
Dendrites
(input)
Axon (output)
White Matter (axons

coated with myelin)
Credit: Santiago Ramon y Cajal: The histology of the Nervous System of Humans and Vertebrates: Publisher: Maloine, Paris, 1911
Pyramidal Neuron
Dendritic branches
Dendritic trunks
Soma (cell body)
Credit: Cerebral Cortex, Volume 1: Editors: Alan Peters and Edward G. Jones: Publisher: Plenum Press: 1984
Cortical Pyramidal Neurons
Credit: Harvard Brain Tissue Resource Center, McLean Credit: Cerebral Cortex, Volume 1: Editors: Alan Peters and Edward G. Jones: Publisher” Plenum Press: 1984
Hospital, Belmont, MA. 1-800-BRAIN BANK
If we took a piece of cerebral cortex from the coronal slice on the left and put it in a silver nitrate (Golgi)
solution, then sliced the block of tissue on a microtome, we would see the pyramidal neurons on the right with
their cell bodies and their dendrite trees ascending up through the cortical layers, branching out to collect
information from other areas of the cortex.
Oligodendrocyte and Nerve Cell Axons
From: “The Human Brain”, Fifth Edition by John Nolte, Publisher: Mosby Inc.: 2002
Myelin is a protein which increases the speed of information flow along axons. Axons are a nerve cell’s
output fiber. The oligodendrocyte on the left is reaching out and wrapping its myelin-filled cell membrane
around two nerve cell axons (labeled A1 and A2). In the right hand picture, we see several axons having
many layers of the membrane wrapped around them, and thus being insulated with many layers of myelin.
Astrocytes
Astrocytes are a type of glial (support) cell that have many functions. They create circuit boxes around
synapses so as to allow and control communication between nerve cells. They coat both nerve cells and
capillaries, thus influencing brain metabolism. They serve as “guide-wires” during the development of the
cerebral cortex and other brain regions, guiding cells to their proper place in the tissue. They also react to
damage caused by neurological diseases, stroke, and trauma. This image shows astrocytes in the retina.
Reactive Astrocytes
These astrocytes are reacting to the damage done by Huntington’s Disease. The nuclei of the
astrocytes are stained with a dye called Hematoxylin, and the astrocytes’ cell body extensions
are stained red with Eosin.
Microglia
Credit: Wai Wong, M.D., Ph.D., staff clinician and chief of the National Eye Institute’s Unit on Neuron-Glia
Interactions in Retinal Disease.
Credit: Samantha Barton, Nature Reviews Neuroscience.

Publisher: Nature Publishing Group: 1996
Microglia are the brain’s surveillance cells. They are part of the immune system and they monitor brain tissue
for signs of disease or tissue damage. When they detect a pathological change, they multiply, migrate to the
diseased or damaged site, and engulf and digest the pathogens and/or cellular debris they find there, in an
attempt to clear the tissue of this material. In the left hand image, microglia (stained green) surrounding blood
vessels (stained red) in the retina of a mouse, search for signs of disease or cell damage. On the right are
microglia (stained blue and green) surrounding and digesting the beta amyloid protein (stained red), that is
found in the senile plaques of Alzheimer’s disease.
The Brain’s Blood Supply
Internal Carotid
Basilar artery artery
External Carotid
artery
Vertebral artery
Common Carotid
artery
Credit Netter’s Atlas of Human Neuroscience: Authors: David L. Felten and Ralph F. Jozefowicz:
Publisher: Icon Learning Systems: 2003
The brain is supplied with blood from four arteries: the two Internal Carotid arteries and the two Vertebral
arteries. Upon reaching the forebrain, the Internal Carotid gives of the Anterior and Middle cerebral arteries.
The two Vertebral arteries reach the ventral surface of the brainstem and give off the first pair of Cerebellar
arteries before coming together to form the Basilar artery. The Basilar artery, in turn, gives rise to two
additional pairs of Cerebellar arteries and the Posterior Cerebral artery.
The Four Arteries That Feed the Brain
Basilar artery
Vertebral artery
Internal Carotid artery

Vertebral artery
Common Carotid
artery
Subclavian
artery
The Aorta
Credit: Magnetic resonance angiography
Author: Ofir Glazer, Bio-Medical Engineering Department, Tel-Aviv University, Israel: 2006
The two Internal Carotid and two Vertebral Arteries

The Vertebral, Basilar, and Cerebellar Arteries
Posterior cerebral artery
Superior Cerebellar artery
Basilar artery
Anterior Inferior
Cerebellar artery
Vertebral artery
Posterior Inferior
Cerebellar artery

The Three Cerebral Arteries and the Circle of Willis

Anterior cerebral artery
Middle cerebral artery Circle of Willis
Basilar artery
Posterior cerebral artery
Vertebral artery
Credit: Neuroanatomy: An Atlas of Structures, Sections, and Systems, Sixth Edition, by Duane E. Haines. Publisher: Lippincott Williams and Wilkins: 2004
Cortical Territories of the Three Cerebral Arteries
From Netter’s Atlas of Human Neuroscience: Authors: David L. Felten and Ralph F. Jozefowicz: Publisher: Icon Learning Systems: 2003
The red branches of the middle cerebral artery cover most of the lateral surface of the cerebral
hemisphere. The purple vessels, stemming from the anterior cerebral artery, feed the medial surface of the
frontal and parietal lobes. The green vessels of the posterior cerebral artery provide blood for the ventral
surface of the temporal and occipital lobes and the medial surface of the occipital lobes. These arteries
provide blood for deeper structures of the cerebral hemisphere as well.
The Cortical Vascular Network
In this electron micrograph, researchers injected plastic into the blood vessels that nourish this
area of cerebral cortex. Then they dissolved the surrounding tissue away with acid, resulting in a
plastic cast of the dense blood vessel network that feeds the cortex.
Veins of the Cerebrum
Credit: Churchill Livingstone, 2002. Credit: www.studyblue.com.
Lateral surface Medial surface
As these two images show, cerebral veins carry blood from the cortex and the deeper regions of the
forebrain into large venous sinuses located in the Dura Mater. From these sinuses, the venous blood
drains into the Internal Jugular veins.
The Brain’s Venous System
Credit: “Multisection CT Venography of the Dural Sinuses and Cerebral Veins by Using Matched Mask Bone Elimination” by:
Majoie C B L M et al. AJNR Am J Neuroradiol 2004;25:787-791
Here, in these MRI images, we can see the veins that drain both the cerebral cortex and the deeper regions
of the brain. These veins flow into a series of large thick venous sinuses located in the Dura Mater. From
these sinuses, the venous blood flows into the Internal Jugular veins and thence to the right atrium of the
heart. Image Description: (a) lateral view, (b) posterior view, (c) dorsal view, (d) oblique view from the right-
rear angle.
Summary of the Brain’s Main Arteries
• Internal carotid arteries

• Anterior cerebral arteries
• Middle cerebral arteries
• Vertebral arteries
– Anterior spinal artery
– Posterior spinal arteries
– Posterior inferior cerebellar arteries (PICA)
• Basilar artery
– Posterior Cerebral Artery
– Anterior inferior cerebellar arteries (AICA)
– Superior cerebellar arteries (SCA)
– Pontine arteries
• Circle of Willis
– Anterior communicating artery
• Connects the anterior cerebral arteries
– Posterior communicating arteries
• Connects the internal carotid and posterior cerebral arteries.
The Structure of an Artery
Lumen Elastic layer
(with red blood cells)
Endothelium
(Tunica Intima)
Muscular layer
Connective tissue
(Tunica Media)
(Tunica Adventitia)
Artery and Vein in the Dura Mater
Artery Vein
A Cerebral Capillary
Cross Section of a Capillary
Endothelial cell
nucleus
Capillary lumen
Credit: A Textbook of Histology, Tenth edition, by Bloom and Faucett:

Publisher: W.B.Saunders Co. 1975
The Brain’s Ventricular System
Credit: Benjamin Cummings, an imprint of Addison Wesley Longman, Inc: 2001
The cerebro-spinal fluid (CSF) is created in and flows through the brain’s ventricles. The flow of CSF
starts in the two large lateral ventricles, then enters the single third ventricle (which separates the
two thalami and hypothalami). From there, the CSF flows through the midbrain’s cerebral aqueduct,
and into the fourth ventricle (lying between the cerebellum and the lower brainstem). The CSF then
flows through apertures in the walls of the fourth ventricle and into the subarachnoid space
surrounding the brain and spinal cord, thereby giving buoyancy and protection to the Central
Nervous System.
A Cast Of The Brain’s Ventricles
Body
Posterior horn
Anterior horn
Third ventricle Fourth ventricle
Inferior horn
Credit: The Human Central Nervous System: A Synopsis and Atlas, by Rudolph Nieuwenhuys et al.: Publisher: Springer Verlag: 2008
The Brain’s Ventricular System
3 2
The above image of a left-half brain exposes the four main regions of the ventricular system: the lateral
ventricle (1), the third ventricle (2), the cerebral aqueduct (3), and the fourth ventricle (4). Normally, the lateral
ventricle would be nearly filled by the striatum (arrow), and so appear much smaller, but since this half brain
is from an advanced case of Huntington’s Disease, the striatum has undergone severe atrophy (shrinkage),
and so has nearly emptied the lateral ventricle, making it much larger than normal.
The Choroid Plexus
The grape cluster-like structure in the ventricles that create the cerebro-spinal fluid is called the choroid plexus.
The Cells of the Choroid Plexus
The cells of the choroid plexus receive blood from capillaries, transform that blood into cerebro-spinal fluid
(CSF), and release the CSF into the ventricles. In this image, the nuclei of the cells are stained purple with
Hematoxylin and the cells’ cytoplasm is stained red with Eosin.
The Hippocampus
Memory formation
The Hippocampus in Context
Credit: The Human Hippocampus by Henri Duvernoy: Publisher: Springer Verlag: 2013
A 3-D dissection of the hippocampus (curved structure) sitting in the lateral ventricle of the temporal lobe.
Exploring the Hippocampus-1
Parahippocampal
gyrus
To see the hippocampus, we first take a coronal slab from the brain, mid-way along the parahippocampal
gyrus in the temporal lobe.
Exploring the Hippocampus-2
On either side of this coronal slab, you can see where the temporal lobes appear to have curled in on
themselves. These are the hippocampi. If we were to remove the right hippocampus (yellow box), cut an
extremely thin tissue section of it and stain the tissue, we would have what we see in the next slide.
A Stained Section of the Hippocampus
The jelly-roll like structure at the center of this image is the hippocampus. It, and the surrounding
structures, are stained with a blue dye that stains the myelin insulation of the nerve cell axons. The red
dye stains the cell cytoplasm and connective tissue. A purple dye stains the cellular nuclei (not seen in this
low-power image).
A Pyramidal Output Neuron of the Rat Hippocampus
The Amygdala
Recognition and evaluation

Fear conditioning
Exploring the Amygdala-1
To see the amygdala, we first take a coronal slab from the brain, near the front of the parahippocampal
gyrus in the temporal lobe.
Exploring the Amygdala-2
On right side of this coronal slab, you can see the round area of grey matter within the yellow box. This is the
amygdala. On the left side of the slab, we see where the amygdala (top) and hippocampus (bottom) overlap. If
we were to remove the amygdala, then section and stain the tissue, we would have what we see in the next
slide.
A Stained Section of the Amygdala
Lateral Ventricle
Amygdala
Hippocampus
Here, the amygdala is left-of-center in this image, left of the lateral ventricle. The blue dye that stains
the thin myelinated fascicles, divides the amygdala into sub-nuclei . The egg-like structure below part
of the amygdala is the beginning of the hippocampus coming into view.
A Neuron from the Amygdala
Credit: The Amygdala, edited by John P. Aggleton: Publisher: Wiley-Liss: 1992
A typical pyramidal neuron from a rat’s amygdala, filled with silver nitrate, using the Golgi stain.
The Spatial Relationship between the Amygdala and Hippocampus
Amygdala
Hippocampus
Credit: Myelin-stained sections from the Yakovlev-Haleem Collection, Washington, DC

Amygdala and Hippocampus
Hippocampus
Amygdala
Credit: The Human Nervous System, edited by George Paxinos: Publisher: Academic Press: 1990
This sagittal section, which is stained for myelin, shows the spatial relationship between the amygdala and
hippocampus. The amygdala is anterior to, and slightly dorsal to the hippocampus in the temporal lobe.
The Striatum
The choreography of context-dependent movement

Motivation, habit, and addiction formation
Exploring the Striatum-1
The striatum
A portion of the striatum is seen filling the lateral ventricle in a medial view of a left half brain.
First, we take a coronal cut through the striatum.

The coronal section that we have created reveals the striatum, here shown as two oval grey matter
structures on either side of the brain, partially filling the lateral ventricles. Next, we remove one block of
the striatum (yellow box), embed the specimen in wax, cut a very thin section, and stain it.
,
Divisions of the Striatum
Caudate nucleus
Putamen
Nucleus Accumbens
The striatum is divided into three regions: the caudate nucleus, (cognitive processing), the putamen (motor
control), and the nucleus Accumbens (motivation).
The Principle Nerve Cell of the Striatum:
The Medium Spiny Neuron
Credit: 'Differential modulation of excitatory and inhibitory striatal synaptic transmission by

histamine', by Tommas J. Ellender et al: Journal of Neuroscience, 2011.
More information converges upon the striatum’s Medium (sized) Spiny Neuron than any other cell in
the nervous system, except the Perkinji cells in the cerebellum. To achieve this, the neuron sends out
dendrites in all directions, each of them loaded with spines which form synapses with large numbers of
other neurons.
The Striatum in Context
Credit: The Human Central Nervous System: A Synopsis and Atlas, by Rudolph Nieuwenhuys et al.:
Publisher: Springer Verlag: 2008
In this drawing, the caudate nucleus (1), following the body of the lateral ventricle, separates from the
putamen (2), arches over the thalamus (3) and enters the temporal horn of the lateral ventricle, where it
combines with the ventral putamen (6).
The Cerebellum
Posture and balance

The coordination of movement
Skill formation
Implicit memory formation
The Cerebellum
Occipital lobe
Ventral surface of
the temporal lobe
Cerebellum
Credit: Harvard Brain Tissue Resource Center, McLean Hospital

Belmont, MA. 1-800-BRAIN BANK
Here, we can see the whole cerebellum attached to the brainstem, and appreciate it’s large size. As the
cerebral cortex has enlarged during primate evolution, so has the cerebellar cortex.
The right cerebellar hemisphere
Cerebellum
The Cerebellar Cortex
This stained section shows why the cerebellum is sometimes called the Arbor Vitae, a Latin phrase meaning
“the tree of life”. The blue stain highlights the myelin (white matter), while the purple (Hematoxylin) and red
(Eosin) stains show the grey matter. Each gyrus in the cerebellum is called a folia (from Latin meaning “leaf”).
The Cerebellar Cortex: a closer view
Molecular
layer
Granule cells
Perkinji cell
layer
This silver-stained section shows the three layers of the cerebellar cortex. The large number of black dots are
the granule cells which receive information into the cerebellum. Then, there is a single layer of giant output
neurons called Perkinji cells. The light-brown region is the molecular layer, where the granule cells pass on
information to the Perkinji cell dendrites.
Cerebellar Perkinji Cells
This image shows the cell bodies of four Perkinji neurons sitting above the very small granule cells, and
sending their dendrites up into the molecular layer, where they will gather information from the granule cell
axons.
The Thalamus
The The gateway to the cerebral cortex

The cerebrum’s central relay station
The Thalamus In Context: The Top of the Brainstem
Thalamus
Midbrain
Pons
Medulla
Credit: The Human Central Nervous System: A Synopsis and Atlas

by Rudolph Nieuwenhuys et al.: Publisher: Springer Verlag: 2008
Exploring the Thalamus-1
Thalamus
Hypothalamus
The thalamus is shown above the hypothalamus, at the top of the brainstem.
First, we take a coronal cut through the diencephalon, which contains the thalamus and hypothalamus.
The coronal section that we have created reveals the two thalami, one on each side of the brain. One
thalamus is shown within the yellow box. Next, we remove that block of tissue, embed it in wax, cut a
very thin section from it, and stain it.
The Thalamus
Internal capsule
Thalamus
Subthalamic nucleus
Substantia Nigra
Mammillary body
This stained section highlights the thalamus along with adjoining structures.
Principle relay neuron of the thalamus
Credit: Jeffery Winer/UC Berkeley-2004)
As shown above, thalamic relay neurons have a large number of information-gathering dendrites that
collect information from the brainstem, process this information, and project the results to the
cerebral cortex.
Thalamo-Cortical Projection Map
Credit: Netter’s Atlas of Human Neuroscience: Authors: David L. Felten and Ralph F. Jozefowicz:
Publisher: Icon Learning Systems: 2003
Each color-coded subdivision of the thalamus projects to and excites a different part of the cerebral cortex.
The Hypothalamus
Homeostasis
Hormonal regulation
Autonomic control
Instinctual drives
Pituitary gland control
Location of the Hypothalamus
Thalamus
Hypothalamus
The hypothalamus is shown below the thalamus.

The Ventral Surface of the Hypothalamus
Olfactory tract
Optic nerve
Optic chiasm
Pituitary stalk
Optic tract
Mammillary bodies
This is a close-up view of a ventral surface of the hypothalamus, which extends from the optic chiasm to and
including the mammillary bodies. The pituitary gland normally hangs off of the pituitary stalk.
Hypothalamic Nuclei
The hypothalamus is divided into many sub-divisions called nuclei. Each of these nuclei secretes different
hormones and performs different functions. Many of them produce compounds that control the pituitary gland’s
secretions. In the following four images, we will use the Supra-Optic Nucleus (labeled “SO” in the above
diagram) as an example of a hypothalamic nucleus and the hormones that it creates.
Finding the Supra-Optic Nucleus of the Hypothalamus (1)
First, we take a coronal cut through the anterior diencephalon.

Finding the Supra-Optic Nucleus of the Hypothalamus (2)
Optic tract
The coronal section that we have created reveals the two sides of the hypothalamus, located just above and
between the white matter of the optic tracts, within the yellow box. If we cut and stain one side of this area, we
will see the supra-optic nucleus above the optic tract.
The Supra-Optic Nucleus
Supra-optic
nucleus
Optic tract
Luxol Fast Blue-Hematoxylin-Eosin stain, 20X
The supra-optic nucleus produces, among other substances, Anti-Diuretic Hormone (ADH), which, by
influencing the kidneys, helps maintain the body’s water balance, and therefore blood pressure.
Neurons of the Supra-Optic Nucleus
Hematoxylin-Eosin stain, 200X
This is an up-close view of the neurons that make up the supra-optic nucleus, and which produce
ADH/Vasopressin.
The Relationship between the Hypothalamus and Pituitary gland
Credit: www.acbrown.com
As the above diagram shows, the pituitary gland is attached to the hypothalamus by the pituitary stalk. The
Supra-Optic and Periventricular nuclei in the hypothalamus produce the hormones Oxytocin and
Vasopressin, that their axons deliver to the Posterior Pituitary. There, the axons release these hormones
into the blood stream. Other hypothalamic neurons secrete “controller” hormones into blood vessels that
bring these hormones to the Anterior Pituitary, where they stimulate (or inhibit) the Anterior Pituitary’s
glandular tissue to produce and release its hormones into the blood-stream. Each hormone produced by
the Anterior Pituitary is under the control of specific controller hormones from the hypothalamus.
The Pituitary Gland
This is a low power microscopic image of the Pituitary Gland (also called the Hypophysis). The left-hand
side of the image is the Posterior Pituitary (the Neurohypophysis), composed of nerve cell axons
emanating from the hypothalamus (specifically the Supra-Optic and Periventricular nuclei). The central
portion of the Pituitary (the Pars Intermedia) consists of cysts that are remnants of the tissue that gave rise
to the Anterior Pituitary. The right side of the image shows the Anterior Pituitary (the Adenohypophysis),
composed of glandular tissue that also produces and delivers hormones into the blood-stream.
The Pituitary Gland
This is a higher magnification image of the anterior pituitary gland. Hematoxylin stains the cell nuclei purple.
Eosin stains the cells’ cytoplasm very light pink (basophilic cells) or dark red (acidophilic cells). These
glandular cells could be further sub-divided if we were to employ techniques that stain the specific hormone
produced by a given cell.
The Brainstem
• The brainstem is, in many ways, the most fascinating part of the entire nervous system. It is
packed with nerve cell groups (nuclei), fiber pathways, and functional regions. The
brainstem serves as an information conduit between the brain and spinal cord, contains
most of the cranial nerves and their nuclei, produces many of the brain’s chemical
messengers (neurotransmitters), such as dopamine, noradrenalin, and serotonin, and has
control centers for basic bodily functions such as respiration, cardiac rhythms, urination,
bowel movements, and sexual functions. It also produces fibers that reach up into the
forebrain, bringing the cerebral cortex into a state of arousal, and therefore allowing
consciousness, sensory experience, memory, attention, learning and motor activity to exist.
Finally, it is the central reflexive and integration center of the brain.
• Although a complete examination of the brainstem is well beyond the scope of this
introduction, we will, in the following images, look at selected brainstem structures that will
give us an idea of how much the brainstem accomplishes.
The Brainstem’s Divisions
Midbrain
Pons
Medulla Credit: Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, MA.
Credit: Neuroanatomy: Text and Atlas by John H. Martin.

Three Cranial Nerves for Eye Movements
Cerebrum
Oculomotor nerve (3)
Trochlear nerve (4)
Abducens nerve (6)
Cerebellum
From: “The Human Brain”, Fifth Edition by John Nolte, Publisher: Mosby Inc.: 2002
Here, we can see many cranial nerves emerging from the brainstem. Cranial nerves number 3, 4, and 6 (the
Oculomotor, Trochlear, and Abducens nerves) control the muscles that move our eyes in their sockets.
Exploring the Midbrain
Credit: Neuroanatomy: Text and Atlas by John H. Martin.

If we take a transverse cut through the midbrain, then stain a slice of this region, we will see the following
stained slice, and identify many of the structures there.
A Transverse Slice through the Midbrain
1
7
3
6
5
4
In this stained slice, we find: (1) the Inferior Colliculus, a brainstem relay station for hearing. (2) The Medial
Longitudinal Fasciculus, carrying fibers that coordinate the movement of our eyes, head, and neck as we
respond to visual or auditory stimuli. (3) The Medial Lemniscus relays the sensations of touch and proprioception
to our forebrain. (4) The Cerebral Peduncle delivers information from the cerebral cortex to the cerebellum and
motor commands to our spinal cord. (5) The Substantia Nigra produces the chemical messenger dopamine. (6)
The Superior Cerebellar Peduncles carry information from the cerebellum to the cerebral cortex. (7) The
Cerebral Aqueduct passes cerebrospinal fluid it to the lower brainstem’s fourth ventricle.
The Substantia Nigra
Substantia Nigra
Among it’s many functions, The Substantia Nigra synthesizes the chemical neurotransmitter Dopamine.
Dopamine is involved in producing smooth motor activity.
Dopamine is also involved in the brain’s motivation and reward systems, and therefore addictions.
Dopamine is also necessary for attention, a major requirement for learning and reaching rewards.
The Substantia Nigra and Parkinson’s Disease
Normal Parkinson’s Disease
On the left is a low-power image of the Substantia Nigra, where we notice a large number of nerve cells which
produce the neurotransmitter Dopamine. On the right is another low-power image of the Substantia Nigra from
a case of Parkinson’s Disease, where most of the Dopamine-producing neurons have disappeared.
Luxol Fast Blue-Hematoxylin-Eosin stain 20x magnification

The Substantia Nigra and Parkinson’s Disease
Normal Luxol Fast Blue-Hematoxylin-Eosin stain 400x magnification Parkinson’s
On the left, we see a higher-power image of the Substantia Nigra. The healthy neurons have large amounts
of neuromelanin, a by-product of dopamine synthesis. On the right is an image of the Substantia Nigra from a
case of Parkinson’s Disease, where we find one remaining neuron containing little neuromelanin (indicative of
little dopamine synthesis), and two Lewy Bodies, the hallmark of the disease.
Locating the Dorsal Raphe Nucleus
Location of the dorsal

raphe nucleus Medial longitudinal
fasciculus
Luxol Fast Blue-Hematoxylin-Eosin stain, (1x)
In this transverse section of the midbrain, we saw the dopamine-producing Substantia Nigra. Now we are also
beginning to see the location of the Dorsal Raphe Nucleus, one of seven groups of nerve cells that produce
Serotonin. It is located in the small trough between the pair of myelinated Medial Longitudinal Fasciculi.
Location of the Dorsal Raphe Nucleus
The Dorsal Raphe

Nucleus
Here is a higher magnification, showing the location of the Dorsal Raphe Nucleus, in the space between the
bundles of myelinated nerve fibers of the Medial Longitudinal Fasciculi. However, we still cannot see the
individual neurons of the Dorsal Raphe Nucleus. For that, we need to utilize the Cresyl Violet dye that stains
the nerve cell bodies in the following image.
Dorsal Raphe neurons
In this image, we can clearly see the big individual neurons of the Dorsal Raphe Nucleus.
The Raphe Pontis
Bielschowsky silver stain (400X)
This image shows the neurons of another Raphe nucleus, the Raphe Pontis (in the Pons region of the
brainstem), this time stained with silver nitrate.
Exploring the Pons
Credit: Neuroanatomy Text and Atlas by John H. Martin; Appleton and Lange, Publishers
Transverse section through the Pons

Exploring the Pons
2 3
4
5
Credit: Neuroanatomy: An Atlas of Structures, Sections, and Systems, Sixth Edition, by Duane E. Haines. Publisher: Lippincott Williams and Wilkins
In this myelin-stained section of the Pons we can see, from top to bottom: (1) the fourth ventricle, which
receives cerebrospinal fluid (CSF) from the midbrain’s cerebral aqueduct; (2) the Medial Longitudinal
Fasciculus, carrying fibers that integrate the movements of our eyes, head, and neck; (3) the Superior
Cerebellar Peduncle, carrying information from the cerebellum to the forebrain; (4) the Middle Cerebellar
Peduncle, delivering information from the cerebral cortex to the Pontine Nuclei (5), which in turn relays this
information to the cerebellar cortex, and (6) the Cortico-Spinal Tracts, carrying motor commands from the
cerebral cortex to the spinal cord.
The Locus Coeruleus and Noradrenalin
Locus Coeruleus
Credit: Neuroanatomy: An Atlas of Structures, Sections, and Systems, Sixth Edition, by Duane E. Haines. Publisher: Lippincott Williams and Wilkins
The Locus Coeruleus (from the Latin, meaning “the blue place”) synthesizes the chemical
neurotransmitter Noradrenalin (Norepinephrine). The Locus functions as part of the brainstem’s system
that brings the cerebral cortex into a state of arousal, which makes consciousness possible. The Locus
Coeruleus and adjacent brainstem areas also control regions in the spinal cord regarding defecation,
urination, and sexual functions. Noradrenalin increases the base level of the brain’s activity and
stimulates the sympathetic nervous system, inducing the so-called “fight or flight” response.
The Locus Coeruleus
Luxol Fast Blue-Hematoxylin-Eosin stain 20x
Parkinson’s Normal
On the right, we see a low-power image of the Locus Coeruleus (arrow), the group of nerve cells which
produce the neurotransmitter Noradrenaline. On the left is another low-power image of the Locus
Coeruleus from a case of Parkinson’s Disease, where most of the Noradrenalin-producing neurons
have disappeared .
The Locus Coeruleus
Luxol Fast Blue-Hematoxylin-Eosin stain 400x
Parkinson’s Disease Normal
On the right, we see a higher power image of the Locus Coeruleus, with nerve cells containing plenty of
neuromelanin, a by-product of noradrenalin synthesis. On the left is another image of the Locus Coeruleus
from a case of Parkinson’s Disease, where most of the neurons are pale, having lost most of their
neuromelanin or have Lewy Bodies (arrows), the pathological hallmark of the disease.
The Pontine Nuclei
Credit: Neuroanatomy Text and Atlas by John H. Martin; Appleton and Lange, Publishers
The Pontine Nuclei
1
3 2
4
6
5
Credit: Cresyl Violet stained Pons from the Yakovlev-Haleem Collection, Washington, DC
In the lower Pons are great numbers of neurons called the Pontine Nuclei. These cells receive information
from the cerebral cortex, process this information, and then relay it to the cerebellum. The above image shows
the transverse white matter fibers (unstained) carrying information into and out of the lower Pons. The Pontine
Nuclei (stained purple), serve as an interface between the way motor information is handled in the cerebral
cortex, and the way it is handled in the cerebellar cortex. In this stained slice of brainstem, we find (1) Fourth
Ventricle, (2) Cerebellum, (3) Superior Cerebellar Peduncle, (4) Medial Lemniscus, (5) Pontine Nuclei, (6)
Transverse Pontine Fibers, and (7) Cortico-Spinal Tract fibers.
.
Histology of the Pontine Nuclei
Luxol Fast Blue-Hematoxylin-Eosin stain (100X) Cresyl Violet stain (100X)

Histology of the Pontine Nuclei

Exploring the Medulla
Credit: Neuroanatomy Text and Atlas by John H. Martin: Credit: Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, MA.
Appleton and Lange, Publishers Luxol Fast Blue-Hematoxylin-Eosin stain, 1X
When we take a transverse cut through the Medulla (formally named the Medulla Oblongata), we have the
resulting stained section.
Exploring the Medulla
6 7 8
4 5
3
2
1
Here we find (1) the pyramidal tracts, carrying motor commands to our spinal cord; (2) the Inferior Olivary
Nucleus, projecting excitatory fibers to the cerebellum; (3) the Medial Lemniscus, relaying tactile and
proprioceptive sensory information to the forebrain; (4) the Reticular Formation, the brain’s central integration
and reflexive center; (5) the Medial Longitudinal Fasciculus, allowing coordinated movement of our eyes, head,
and neck; (6) the Solitary Tract, carrying visceral-sensory information from our internal organs; (7) the grey
matter region containing many cranial nerve nuclei; (8) the fourth ventricle, receiving cerebro-spinal fluid (CSF)
from the cerebral aqueduct.
Three Cranial Nerve Nuclei
Luxol Fast Blue-Hematoxylin-Eosin stain, 20x
Near the dorsal (top) surface of the Medulla, we find three cranial nerve nuclei. The Solitary Nucleus
receives viscero-sensory information from our internal organs via the Solitary Tract. The Dorsal Motor
Nucleus of the Vagus Nerve projects viscero-motor commands to our internal organs via the Vagus Nerve.
The Hypoglossal Nucleus innervates the muscles of our tongue.
The Solitary Nucleus, Solitary Tract, and Area Postrema
3
2 2
1
4
1
4
Luxol Fast Blue-Hematoxylin-Eosin stain (20X and 200X)
These two sections of the medulla show the Solitary Tract (1), the Solitary Nucleus (2), the Area Postrema
(3), and the Dorsal Motor Nucleus of the Vagus Nerve (4).
The Area Postrema
Luxol Fast Blue-Hematoxylin-Eosin stain (400X)
This is a close-up image of the Area Postrema. It is a region that receives vomit-inducing information from
the gastro-intestinal tract via the Vagus Nerve. It also serves as a chemical-sensing center that triggers the
vomiting reflex in response to vomit-inducing substances in our blood. It is composed of connective tissue,
blood vessels and sensory neurons.
The Histology of the Inferior Olivary Nucleus
The above two images show two magnifications of the Inferior Olivary Nucleus, located in the lower medulla.
The fibers streaming out of its center toward the right are heading toward the cerebellar cortex where they
will cover the cerebellar Perkinji neurons with what are termed “climbing fibers”, providing highly excitatory
stimulation to the Perkinji cells, which is thought to help “train” the Perkinji cells into producing the proper
coordinated firing that will result in coordinated motion in us. The Inferior Olivary Nucleus is part of what is
called the “cerebellar system”.
Olivary Climbing Fibers adorning a Perkinji Cell Dendritic Tree.
Credit: Santiago Ramon y Cajal: The Histology of the Nervous System in Humans and Vertebrates: Publisher: Maloine, Paris, 1911
Cerebellar Perkinji cell Olivary climbing fiber
The left hand image shows a single Perkinji cell from the cerebellar cortex. The right hand image shows a
single climbing fiber from the Inferior Olivary Nucleus covering the Perkinji cell’s dendritic tree.
The Reticular Formation
1
1
In the center of the upper Medulla (1), and along the entire length of the brainstem, lies the brainstem’s very
core, the Reticular Formation. The image on the right shows why the area bears this name. It is a mesh-work
of nerve fibers containing large numbers of nerve cell bodies. The Reticular Formation can be divided into
many cellular and functional areas that seem shuffled together, each area connected to every other, producing
a huge interchange of information. The Reticular Formation has control centers for basic functions such as
respiration, cardiac rhythms, urination, bowel movements, sexual functions, pain modulation, sleep, arousal,
and motor activity. As the nervous system’s central integration and reflexive region, it interconnects all of
these functions, so that they work harmoniously together.
Histology of the Reticular Formation
In the last two slides of this presentation, we see two increasing magnifications of the Reticular Formation.
The left-hand images show staining of the region with a Myelin-Hematoxylin-Eosin stain.
The right-hand images utilize the Cresyl Violet dye that stains the nerve cells purple.
Histology of the Reticular Formation

Acknowledgements
In creating this Introduction to Neuroanatomy as a completely non-profit, educational-

only experience, we at the Harvard Brain Tissue Resource Center have supplemented the images
generated by our own department with those from the atlases and papers of other anatomists and
researchers. Please find these acknowledgments under their respective images. Thank you.
THE END
We at the Harvard Brain Tissue Resource Center hope that you have enjoyed this
introduction to human neuroanatomy, and that it has proven informative and useful. Please feel
free to relay any questions, comments, or suggestions that you may have. Thank you.

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An Introduction To

• The brain’s surfaces

Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, MA.

Ventral Posterior (caudal) Medial

Credit: “The Human Brain” by Henri M. Duvernoy, Publisher: Springer-Verlag/Wien; 1999.

• Third picture: Dividing the whole brain into a half-brain.

• Fifth picture: A cerebral hemisphere.

Left Half brain

A cerebral hemisphere is a half brain with the brainstem removed

• The Dura Mater ( Latin for “Tough mother”, as in durable)

• The Arachnoid layer (Spider-like layer)

• The Sub-arachnoid space

• The Pia Mater (Latin for “Tender mother”)

Image credit:http://www.profelis.org/vorlesungen/neuroanatomy_1ns.html: 2013

Image credit:http://www.profelis.org/vorlesungen/neuroanatomy_1ns.html: 2013

Image credit:http://www.profelis.org/vorlesungen/neuroanatomy_1ns.html: 2013

Credit: “The Human Brain” by Henri M. Duvernoy, Publisher: Springer-Verlag/Wien; 1999.

Credit: “The Human Brain” by Henri M. Duvernoy, Publisher: Springer-Verlag/Wien; 1999.

Arachnoid layer Dura Mater

Pia mater Brain tissue

Grey matter White matter

• Neurons (nerve cells)

Cell Body (soma)

White Matter (axons

Soma (cell body)

Credit: Samantha Barton, Nature Reviews Neuroscience.

Internal Carotid artery

The two Internal Carotid and two Vertebral Arteries

Internal Carotid artery

Posterior cerebral artery

Superior Cerebellar artery

Credit: “The Human Brain” by Henri M. Duvernoy, Publisher: Springer-Verlag/Wien; 1999.

Internal Carotid artery

Middle cerebral artery Circle of Willis

Posterior cerebral artery

Credit: “The Human Brain” by Henri M. Duvernoy, Publisher: Springer-Verlag/Wien; 1999.

Credit: Churchill Livingstone, 2002. Credit: www.studyblue.com.

Lateral surface Medial surface

• Internal carotid arteries

Credit: A Textbook of Histology, Tenth edition, by Bloom and Faucett:

Credit: Benjamin Cummings, an imprint of Addison Wesley Longman, Inc: 2001

Third ventricle Fourth ventricle

Recognition and evaluation

Credit: The Amygdala, edited by John P. Aggleton: Publisher: Wiley-Liss: 1992

Credit: Myelin-stained sections from the Yakovlev-Haleem Collection, Washington, DC

The choreography of context-dependent movement

First, we take a coronal cut through the striatum.

Credit: 'Differential modulation of excitatory and inhibitory striatal synaptic transmission by

Posture and balance

Credit: Harvard Brain Tissue Resource Center, McLean Hospital

The The gateway to the cerebral cortex

Credit: The Human Central Nervous System: A Synopsis and Atlas

Credit: Jeffery Winer/UC Berkeley-2004)

The hypothalamus is shown below the thalamus.

Credit: “The Human Brain” by Henri M. Duvernoy, Publisher: Springer-Verlag/Wien; 1999.

First, we take a coronal cut through the anterior diencephalon.

Luxol Fast Blue-Hematoxylin-Eosin stain, 20X

Hematoxylin-Eosin stain, 200X

Hematoxylin-Eosin stain, 20X

Credit: Neuroanatomy: Text and Atlas by John H. Martin.

Trochlear nerve (4)

Abducens nerve (6)

Credit: Neuroanatomy: Text and Atlas by John H. Martin.