HBF-III LEC 22 Neuroscience Anatomy Brainstem Notes 2025 Walker PDF

Neuroscience: Anatomy of the Brainstem Page 1 of 18 Dr. Paul Walker Session Objectives By the end of this session, students should be able to accurately: 1. Discuss the functional organization of the brainstem. 2. Recognize brainstem cros...

Neuroscience: Anatomy of the Brainstem Page 1 of 18 Dr. Paul Walker Session Objectives By the end of this session, students should be able to accurately: 1. Discuss the functional organization of the brainstem. 2. Recognize brainstem cross sections and correctly identify structures within each level. 3. Identify brainstem regions in medical images. 4. Identify structures of the diencephalon and discuss relations with the telencephalon. Session Outline I. Functional Organization of the Brainstem II. Cross Sectional Anatomy of the Brainstem III. Recognizing Brainstem Regions in Medical Images IV. Diencephalon and Relationships with the Telencephalon Supplemental Reading Fundamental Neuroscience for Basic & Clinical Applications, 5 th Ed (2018) Haines & Mihailoff. Elsevier. Ch 10 Overview of the Brainstem. https://www-clinicalkey- com.proxy.lib.wayne.edu/#!/content/book/3-s2.0- B9780323396325000268?indexOverride=GLOBAL Nolte’s The Human Brain, 8th Ed (2021), TW Vanderah & DJ Gould, Elsevier. Ch. 11 Organization of the Brainstem. https://www.clinicalkey.com/#!/content/book/3-s2.0- B9780323653985000199?indexOverride=GLOBAL Neuroscience: Anatomy of the Brainstem Page 2 of 18 Dr. Paul Walker I. Functional Organization of the Brainstem 3 Functions of the Brainstem Fig 1 Nolte 1. Conduit for sensory and motor pathways, and houses relay networks for these pathways. 2. Location of cranial nerve nuclei and associated circuits for head and body functions. 3. Contains neural networks that integrate different functions according to sensory and motor information relayed. Some of these networks are part of the reticular formation. Dashed line in Fig 1 indicates the approximate level of a cut to divide the midbrain from the diencephalon. The diencephalon is part of the brainstem, but the brainstem is often discussed as the midbrain, pons, and medulla. The cerebellum is derived from the pons but is a separate system. Fig 2 Nolte General Boundaries Midbrain Line at posterior commissure to line at superior pontine sulcus. Pons Line at superior pontine sulcus to line at inferior pontine sulcus Medulla Line at inferior pontine sulcus to line at foramen magnum Related Structures Midbrain Ventral: Cerebral peduncles& interpeduncular fossa Dorsal: Cereral aqueduct & tectum Pons Cranial Nerve Relations Ventral: Basal pons Midbrain Dorsal: Main part of 4th ventricle & cerebellum CN III, IV Medulla Pons Ventral: Pyramids CN V, VI, VII, VIII Dorsal: Caudal part of 4th ventricle & cerebellum Medulla CN VIII, IX, X, XII *CN XI –cervical spinal cord, CN II- diencephalon, CN I- telencephalon Neuroscience: Anatomy of the Brainstem Page 3 of 18 Dr. Paul Walker Fig 3 Nolte The tegmentum refers to a region of the brainstem that contains the cranial nerve nuclei and a neural network called the reticular formation. The tegmentum extends through the midbrain, pons, & medulla. Tegmentum is derived from tegumentum (L- a covering, shell, or husk). In the midbrain, the tegmentum is distinguished from the tectum dorsally and the cerebral peduncles ventrally. In the pons, the tegmentum is distinguished from 4th ventricle dorsally and the basal (basilar) pons ventrally. In the medulla, the tegmentum is distinguished from large sensory nuclei and 4th ventricle dorsally and a large descending motor pathway called the pyramidal tract ventrally. Fig 4 Nolte In a dissected brainstem with the cerebellum removed (does not include diencephalon), there are several landmarks that can be distinguished. Midbrain Dorsal (Fig 4 left) Tectum contains the superior colliculus (SC) and inferior colliculus (IC). CN IV can be seen at the junction between midbrain and pons. Ventral (Fig 4 right) Cerebral peduncles (CP) and the interpeduncular fossa with CN III emerging. Pons Medulla Dorsal (Fig 4 left) Dorsal (Fig 4 left) 3 cerebellar peduncles: superior Floor of 4th ventricle in open medulla (rostral) (SCP), middle (MCP), inferior (ICP) Tuberculum gracilis and tuberculum cuneatus in closed and the floor of the 4th ventricle medulla (caudal) form large bumps on dorsal surface. Ventral (Fig 4 right) Ventral (Fig 4 right) Basal pons (BP) and CN V, VI, VI, Pyramids formed by underlying pyramidal tract. VIII. Olive formed by underlying inferior olivary nucleus. Inferior pontine sulcus is clear boundary between medulla and pons. CNs IX, X, XI, XII. Neuroscience: Anatomy of the Brainstem Page 4 of 18 Dr. Paul Walker Fig 5 Nolte One goal of this lecture is to learn to recognize different brainstem levels in cross section and associate certain structures at each level. This becomes important when interpreting medical images that may show evidence of damage in specific regions. The above Fig 5 shows different levels of each brainstem region. We will begin analyzing cross sections at the caudal end of the brainstem at the level of the foramen magnum and work our way rostrally toward the diencephalon. We will pass through the medulla, pons, and midbrain and learn to recognize characteristics of each region. Below Fig 6 emphasizes how the gray and white matter appearance of the spinal cord changes as we take sections through the caudal end of the brainstem (caudal medulla). The normal H-shaped gray matter of the spinal cord surrounded by white matter tracks transitions to a different look when we cross into the medulla. Fig 6 Neuroscience: Anatomy of the Brainstem Page 5 of 18 Dr. Paul Walker II. Cross Sectional Anatomy of the Brainstem Let’s analyze cross sections of the brainstem one at a time and learn the distinguishing features of each. We’ll begin with the most caudal section of the medulla. Fig 7 Fig 7 shows a transverse section through the brainstem at the level of the foramen magnum. This would cut through the caudal medulla at the level of the decussation of the pyramidal tract. In this section, the dorsal surface of the medulla resembles the spinal cord and is called the closed medulla. There are 3 sensory nuclei & tracts (dorsal) Nucleus Gracilis (NG) & Fasciculus Gracilis (FG) Nucleus Cuneatus (NC) & Fasciculus Cuneatus (FC) Spinal Nuc V (SpN V) & Spinal Tract V (SpT V) The 3 sensory nuclei and associated tracts convey touch information from the body (NG, NC) and pain information from the face (SpN). The ventral part of the section is dominated by the pyramidal tracts, which cross the midline at this level and end up in the lateral funiculus of the cervical spinal cord. Neuroscience: Anatomy of the Brainstem Page 6 of 18 Dr. Paul Walker Fig 8 Fig 8 shows a transverse section through the caudal medulla. The dorsal surface is still in the closed position and resembles the round shape of the spinal cord. This will soon change as we progress more rostrally in the medulla. The 3 sensory nuclei & tracts are still present dorsally, but the associated tract for NG is less obvious. Again the 3 sensory nuclei & tracts are: Nucleus Gracilis (NG) & Fasciculus Gracilis (FG) Nucleus Cuneatus (NC) & Fasciculus Cuneatus (FC) Spinal Nuc V (SpN V) & Spinal Tract V (SpT V) The pyramidal tract (PT) makes up a large part of the ventral region of the medulla. Just dorsal to the PT is a swirling piece of gray matter. It is the caudal end of the inferior olivary nucleus (ION) that will become larger in more rostral sections of the medulla. The tegmentum of the medulla at this level is anything dorsal to the PT and ION. Neuroscience: Anatomy of the Brainstem Page 7 of 18 Dr. Paul Walker Fig 9 At this mid-medulla level (Fig 9), the dorsal edge of tissue is pushed laterally because of the 4 th ventricle. The gray matter that comprises the floor of the 4th ventrice is called periventricular gray and contains an important parasympathetic nucleus. It is called the Dorsal Motor Nucleus of X (Vagus) that contains the cell bodies of preganglionic PANS neurons that we have been studying in the HBF-II course. Ventrolateral to DM-X is the Solitary Nucleus (Sol) that surrounds the white matter of the solitary tract. The Sol nucleus and tract provide important visceral afferent (sensory) information carried by the vagus nerve about the cardiovascular and respiratory systems and the gastrointestinal system. The Hypoglossal Nucleus (H) is located medially and contains the somatic efferent motor neurons that project to the tongue musculature. We’ve reached the rostral extent the dorsal sensory nuclei observed in the caudal medulla. Nucleus gracilis is not present in the mid-medulla, but a small rostral portion of nucleus cuneatus is still located dorsally (unlabeled in this section). Spinal Nuc V (SpN V) & Spinal Tract V (SpT V) are still located laterally at this level and there is a growing mass of white matter on the dorsolateral surface of the medulla. This is the inferior cerebellar peduncle (unlabeled) that will become larger in more rostral sections. Ventrally, the inferior Olivary Nucleus (ION) resembles a leaf shape. The nucleus ambiguus (Amb) is located between SpN V and ION and is a Special Visceral Efferent (SVE) nucleus that projects to laryngeal and pharngeal muscles innervated by CN X. Pyramidal Tract (PT) is still located ventrally. The tegmentum at this mid-medulla level is anything dorsal to the ION and PT. Neuroscience: Anatomy of the Brainstem Page 8 of 18 Dr. Paul Walker Fig 10 The dorsal surface of the rostral medulla is fully open and provides a gray matter floor of the 4th ventricle. The Vestibular Nucleus (VN) and Cochlear Nucleus (CN) are positional dorsally with the VN medially and the CN laterally. The VN and CN are part of (CN VIII). The solitary (Sol) nucleus and tract (nucleus surrounds tract) are still present at this level. The Inferior Salivatory Nucleus (ISN) is located medial to Sol. It contains preganglionic parasympathetic neurons that regulate the parotid gland. The Inferior Cerebellar Peduncle (ICP) has amassed heavily myelinated afferents to the cerebellum and is present laterally. The spinal nucleus and tract of V are covered by white matter associated with the ICP. The Nucleus ambiguus (Amb) is located between SpN V and the inferior olivary nucleus (ION) and at this level contains the SVE cell bodies of glossopharyngeal nerve efferents projecting to the pharynx. The pyramidal tract (PT) is located ventrally. Anything dorsal to the PT and ION is the tegmental region of the rostral medulla (bounded dorsally by the 4 th ventricle). Neuroscience: Anatomy of the Brainstem Page 9 of 18 Dr. Paul Walker Fig 11 There are distinguishing features of the pons that allow its identification. First, the ventral region is dominated by the basal (basilar) pons, which contains structures related to cerebellar function. One such structure is the transverse pontine fibers that course perpendicular to the long axis of the brainstem and interrupt the fibers of the PT. The gray matter in the basal pons is made up of scattered nuclei known as pontine nuclei. Their function is tied to the cerebellum. A line shown in the image divides the basilar pons ventrally from the tegmentum pons dorsally. The pontine tegmentum at this level contains some important cranial nerve nuclei as well as other nuclei and passing white matter tracts. The Abducens Nucleus (Ab) and Facial Motor Nucleus (F) are located at this level, along with their corresponding nerve roots (VI, VII) coursing through the tissue. The F nucleus is another SVE nucleus and delivers motor signals to muscles of facial expression, among other muscles we’ll learn in this course. Another nucleus related to the auditory pathway is called the Superior Olivary Complex (SOC) and also serves as a landmark for caudal pons. This is also the most rostral extent of the spinal nucleus and tract of V. The rostral extent of the vestibular nucleus (V) is also at this level located laterally in the walls of the 4 th ventricle. Large cerebellar peduncles are observed dorsolaterally and are comprised of superior cerebellar pedunce (SCP), middle cerebellar peduncle (MCP), and inferior cerebellar peduncle (ICP). We saw the ICP at mid- to rostral levels of the medulla and this is the most rostral section that ICP will be visible. MCP is visible at all pons levels (caudal to rostral). SCP is visible here and more rostrally through the pons and into the midbrain. Neuroscience: Anatomy of the Brainstem Page 10 of 18 Dr. Paul Walker Fig 12 The mid-pons is the location of 3 trigeminal nuclei (Trig) 1. Chief Sensory Nucleus of V (Cs)- also called Principal Sensory Nucleus of V 2. Motor Nucleus of V (Mtr) 3. Mesencephalic Nucleus of V (Mes) We will learn how more about the trigeminal nuclei in Neuro Lab 03. Cs is the main nucleus for discriminatory touch sensations from the face/head. Mtr is the main SVE nucleus that delivers motor commands to mastication muscles and other muscles of the head that we’ll learn in this course. Mes is the main nucleus for proprioceptive feedback (e.g. jaw-jerk reflex, how hard to bite down on food). Although not visible in the section, the trigeminal nerve (CN V) with its 3 divisions (V1 ophthalmic, V2 maxillary, and V3 mandibular) would be located on the lateral surface of the basilar pons. The motor root of V is related to the medial surface of V3 and can be distinguished. The 4th ventricle is bordered dorsolaterally by the SCP and the MCP is related laterally to to the basilar pons and transverse pontine fibers. The PT is still located in the basilar pons. The line in the section shows the division between basilar pons ventrally and the tegmental pons dorsally. Neuroscience: Anatomy of the Brainstem Page 11 of 18 Dr. Paul Walker Fig 13 In this section through the rostral pons, the tegmentum is known as the isthmus because it has narrowed to its smallest size. The yellow line marks the division between basilar pons ventrally and tegmental pons dorsally. The 4th ventricle has also narrowed and will merge with the cerebral aqueduct at the level of the caudal midbrain. The gray matter that borders the 4th ventricle is still called periventricular gray but contains a nucleus known as the locus coeruleus (LC, L: blue spot). The LC contains neurons that produce and release norepinephrine, which is a catecholeamine neurotransmitter. Melanin is a product of catecholamine synthesis and is contained in LC neurons. The collection of neurons in the LC nucleus can be visualized grossly as a dark blue/black spot in this region. The dorsal raphe nucleus (DR) is another well-know nucleus in this region located at midline. DR neurons synthesize and release serotonin, a different type of monaminergic neurotransmitter. Both norepinephrine and serotonin alter mood and affect and will be further discussed in a sequence of neuropharmacology lectures as part of this course. The trochlear nerve (CN IV) is also seen on the dorsal surface of the brainstem at this level. The trochlear nucleus is located in caudal midbrain, but the nerve exits dorsally and decussates such that the trochlear nerve innervates the contralateral superior oblique muscle of the eye as compared to the location of its nucleus. The SCP (superior cerebellar peduncle) is the only cerebellar peduncle visible at this rostral pons level and it will travel rostrally into the midbrain. It is starting to change its position and will decussate in the tegmentum of the caudal midbrain. The pyramidal tract is still coursing through the basilar pons with its fibers dispersed by transverse pontine fibers. Neuroscience: Anatomy of the Brainstem Page 12 of 18 Dr. Paul Walker Fig 14 The caudal midbrain is marked by gray matter that form a roof over the small channel of the cerebral aqueduct (a). The roof is called the tectum of the midbrain. The nuclei of the tectum are so large that they form bumps on the dorsal surface of the tectum. There are 4 bumps total known grossly as the corpora quadrigemina (L: quadruplet bodies). Two of the bumps at this caudal level of midbrain tectum are made by the right inferior colliculus and the left inferior colliculus (IC). The second set of bumps are observed at the level of the rostral midbrain and each is known as the superior colliculus (see Fig 15 on next page). The inferior colliculus (IC) is an important relay nucleus of the auditory pathway that we’ll learn more about in Neuro Lab 04. At this level, the gray matter that borders the cerebral aqueduct is called peraqueductal gray (PAG) in contrast to periventricular gray matter more caudally. No matter- this region still contains the same 2 norepinephrine and serotonin centers- the LC and the DR. Ventral and lateral to the DR lies the trochlear nucleus, which is a landmark for the caudal midbrain. Its nerve root courses laterally and turns dorsally to decussate at midline before exiting the dorsal surface of the tectum. Its root fibers travel caudally which explains why they are visible in sections through the rostral pons (see Fig 13). The SCP dominates the area of the midbrain tegmentum and is seen in full decussation as its fibers are crossing the midline of the caudal midbrain. Depending on the angle of the section, the most rostral portion of the basilar pons is often attached ventrally to the section of caudal midbrain. Similar to other sections shown previously, a yellow line is drawn to separate the tegmentum (this time of midbrain) from the ventral basilar pons. Neuroscience: Anatomy of the Brainstem Page 13 of 18 Dr. Paul Walker Fig 15 The rostral midbrain has many unique structures that enable its identification. Dorsally, the tectum contains a single round nucleus on each side. This is the superior colliculus (SC), which functions as part of the visual system studied in neuro lab 05. The periaqueductal gray (PAG) still surrounds the cerebral aqueduct (a) and now contains the oculomotor nucleus (III) close to the midline. The oculomotor nerve root courses ventrally and exits as the oculomotor nerve (CN III) from the interpeduncular fossa. The interpeduncular fossa is so named because it is between 2 large peduncles of white matter known as the cerebral peduncles (CP). The pyramidal tract is located within the CP along with other axons of passage. Dorsal to the CP is an elongated nucleus known as the substantia nigra (dark substance). While not dark in a Weigert stain, this nucleus appears as a dark stripe in the gross brain because it too contains catecholamine neurons that produce melanin. However these neurons synthesize and release dopamine as part of a basal ganglia circuit that regulates movement. A medial extension of dopamine neurons is called the ventral tegmental area (VTA) which is involved in motivational behaviors. As with the LC and DR, these chemical centers will be discussed in more detail in subsequent neuropharmacology lectures. Dorsal to the SN and VTA is a large round nucleus called the red nucleus (RN). This nucleus has a red tinted appearance in the gross brain and is also related to movement control and has connections with the cerebellum and spinal cord. Laterally, the rostral midbrain merges with caudal diencephalon structures that include the medial geniculate nucleus (MGN) and lateral geniculate nucleus (LGN). The MGN is part of the auditory pathway and the LGN is part of the central visual pathway that we’ll discuss in more detail in Neuro Labs 04-05. Neuroscience: Anatomy of the Brainstem Page 14 of 18 Dr. Paul Walker III. Recognizing Brainstem Regions in Medical Images Fig 16 The main reasons to learn cross sectional anatomy of the brain is to be able to recognize brainstem structures in medical images and also know important structures within each level that may be affected by damage or disease in the patient. In order to master this skill in recognizing images of the brainstem, there’s a strategic hurdle to overcome. First, the brainstem is comparatively small when observed with other head structures. The sections reviewed in previous figures are magnified quite a bit in order to learn the structures. Second, for images obtained in the axial plane, the brainstem image may be upside down as compared to the Weigert stained image on a slide. This is because for histological analysis, brain sections are placed with the ventral side down while axial images of the brain as in Fig 16 are shown the ventral side of the body facing up. Look for the nose in the images in Fig 16, which is on the ventral side of the body. This means that for medical imaging, the anatomy may be flipped upside down in comparison to histological cross sections (Fig 17). Fig 17 Let’s take a look at some images to practice this concept. Neuroscience: Anatomy of the Brainstem Page 15 of 18 Dr. Paul Walker Fig 18 Fig 18 shows 2 identical axial head images at the level of the foramen magnum where the caudal medulla is located. We are inferior to most of the cerebellum (a small portion of the cerebellar tonsils show dorsal to the medulla). The medulla has a round shape similar to the spinal cord. In the right image, a Weigert stained section of caudal medulla has been reduced in size to fit the image and is flipped upside down. The image is shown at higher magnification in the center for your reference. Can you recognize the 3 sensory nuclei dorsally as well as the ventral shape of the pyramids? Fig 19 Fig 19 shows 2 identical axial images of the head at the level of the mid- medulla. The cerebellum is more easily identified dorsal to the small brainstem. The 4th ventricle can be seen and the dorsal surface of the medulla is starting to open. Can you see some features in the image that give you the impression of an upside section of mid-medulla. Can you see the pyramids ventrally and the bump of the olive made by the ION ventrolaterally? Its not easy but you can get a sense of the anatomy by comparing the shape of the medulla to Fig 18 and to the Weigert stained section. Fig 20 Fig 20 shows 2 identical axial images of the head at the rostral medulla level. The cerebellum is present dorsally. The brainstem has a shape characteristic of rostral medulla with prominent inferior cerebellar peduncle on the dorsolateral surface. The pyramids are still observed ventrally. Its not an exact match to the Weigert stained section shown but it is reasonably close to show overlapping characteristics. Neuroscience: Anatomy of the Brainstem Page 16 of 18 Dr. Paul Walker Fig 21 Figure 21 shows 2 identical axial images of the head at the caudal pons level. The cerebellum is present dorsally, but the brainstem shape has changed to fit the image of the caudal pons with all 3 cerebellar peduncles anchoring the brainstem to the cerebellum. The 4th ventricle is visible and this is the region of the abducens and facial nuclei of CNs VI and VII. You don’t have to see the nuclei to know they are present because you can identify this region as caudal pons. Fig 22 Figure 22 shows 2 identical axial images of the head at the rostral pons level. The superior part of the cerebellum is visible, but is bordered by parts of the temporal (lateral) and occipital (posterior) cortices. The shape of the pons resembles the rostral pons with a small isthmus region of the tegmental pons and a large ventral region of basilar pons. The 4th ventricle is present and the decussation of the trochlear nerve can be visualized on the dorsal surface of the brainstem. Fig 23 Figure 23 shows 2 identical axial images of the head at the level of the midbrain. While the Weigert-stained reference image is taken at the level of the superior colliculus, it is possible because of the tilt of axial image that the dorsal surface is at the level of the inferior colliculus and the ventral surface is at the level of the cerebral peduncles. The important point to note is the general shape of the midbrain which resembles ‘Mickey Mouse’. The cerebral peduncles are the ears of the mouse and the face includes both tegmentum and tectum regions of the midbrain at this level. This is characteristic of medical images showing the midbrain. Neuroscience: Anatomy of the Brainstem Page 17 of 18 Dr. Paul Walker IV. Diencephalon & Relationships with the Telencephalon Fig 24 This brings us to the most rostral part of the brainstem called the diencephalon that is surrounded by the telencephalon (Fig 24) Two centers of the diencephalon are the thalamus (dorsal) and hypothalamus (ventral). The thalamus is a major relay station that connects the spinal cord and brainstem to the cerebral cortex. One of its functions is to bring sensations to the level of consciousness. The hypothalamus is a major homeostatic regulator of bodily functions including endocrine, reproductive, ANS, etc. You’ll receive separate lectures on each of these regions later in the course. Axons that carry sensory information from thalamus to the cortex (thalamocortical) travel through a band of white matter called the internal capsule (IC). Other axons also use the internal capsule to travel to and from the cerebral cortex. The thalamocortical axons travel through a particular region: the posterior limb of the internal capsule (PLIC) labeled yellow in below Fig 25. Fig 25 Thalamocortical axons project superiorly into the primary somatosensory cortex located in the parietal cortex. These projections along with others appear like fingers reaching into the cortical gray matter and when dissected resemble a crown. Hence the term corona radiata (CR) for the appearance of the fibers between internal capsule and cerebral cortex. The thalamocortical fibers represent a subset of these fibers (labeled yellow in below Fig 25). Neuroscience: Anatomy of the Brainstem Page 18 of 18 Dr. Paul Walker Fig 26 Cross sections through the thalamus and cerebral cortex in the frontal or coronal plane show gray matter of the cortex on the surface, white matter underneath, and more subcortical gray matter (basal ganglia) or brainstem lies deep. The next 2 cross sections are in the frontal plane indicated by the 2 blue lines in Fig 26. Fig 27 The frontal section shown in Fig 27 is through the caudal diencephalon and catches a portion of the rostral midbrain ventrally. You can visualize the cerebral peduncle, substantia nigra, and red nucleus of the midbrain (encircled in red). The thalamus is encircled in yellow and is at the level of the somatosensory nuclei that convey sensations from the contralateral body and face. Thalamocortical axons from the thalamus to cerebral cortex gather in the posterior limb of the internal capsule (PILC) and are distributed to the primary somatosensory cortex of the parietal lobe via the coronal radiata (CR). Fig 28 In the more rostral frontal section of Fig 28, the thalamus is still present related medially to the PILC. The hypothalamus is positioned ventrally. The plane of the section is rostral to the midbrain, so this region of the brainstem is no longer present in the image. Nuclei of the basal ganglia (part of the telencephalon) are positioned lateral to the PILC at this level. We will have separate neuro labs to study the basal ganglia as well as the thalamus and thalamocortical relationships. This brings us to the rostral extent of the brainstem and ends our tour. I hope you find this information helpful in understanding brainstem sections shown in Neuro Labs 02-03 as well as the interpretation of medical images.