The human brain is the most complex biological structure known — roughly 86 billion neurons forming ~100 trillion synaptic connections, organized into hierarchical functional systems. Understanding its three-dimensional anatomy is essential to neuroscience, neurology, and cognitive science.

 

Major Anatomical Divisions

The brain is traditionally divided into three main regions:

1. Forebrain (Prosencephalon)
Comprises the cerebrum (telencephalon) and the diencephalon (thalamus + hypothalamus). The cerebrum is split into left and right hemispheres, each harboring four lobes. The diencephalon relays sensory and motor signals between the cerebral cortex and the body.

2. Midbrain (Mesencephalon)
The shortest brainstem segment. Its tectum (superior/inferior colliculi) handles visual and auditory orienting reflexes. The tegmentum contains the dopaminergic ventral tegmental area (VTA), red nucleus, and periaqueductal gray for pain modulation.

3. Hindbrain (Rhombencephalon)
Includes the pons, medulla oblongata, and cerebellum. The pons and medulla form the lower brainstem controlling vital autonomic functions (heartbeat, breathing, blood pressure). The cerebellum coordinates voluntary movement and motor learning.

 

The Cerebral Cortex: Four Lobes

The outer gray matter (~2,500 cm² unfolded, 2–4 mm thick) is organized into four lobes in each hemisphere:

Lobe	Location	Key areas & functions
Frontal	Anterior to central sulcus	Primary motor cortex, prefrontal cortex, Broca’s area — voluntary movement, executive function, working memory, speech production
Parietal	Posterior to central sulcus	Primary somatosensory cortex (homunculus), posterior parietal cortex — touch, visuospatial awareness, attention
Temporal	Inferior to lateral sulcus	Primary auditory cortex (Heschl), Wernicke’s area, hippocampus/amygdala — hearing, language, memory, emotion
Occipital	Most posterior	V1 (striate cortex) + extrastriate V2–V5 — vision, feeding the dorsal “where” and ventral “what” streams

 

Subcortical and Limbic Structures

Structure	Role
Thalamus	“Gateway to the cortex” — relays all sensory modalities except olfaction (LGN→V1 vision, MGN→A1 hearing, VPL→S1 touch/pain).
Hypothalamus	Homeostasis — feeding, temperature, circadian rhythm (suprachiasmatic nucleus), and pituitary hormone control.
Hippocampus	Memory encoding via the trisynaptic circuit (entorhinal → dentate gyrus → CA3 → CA1); theta (4–8 Hz) supports spatial navigation.
Amygdala	Fear/emotion — basolateral complex takes sensory input; central nucleus drives autonomic fear responses via hypothalamus and brainstem.

 

Basal Ganglia: Action Selection Circuit

The basal ganglia form the cortico-striato-thalamo-cortical (CSTC) loop:

The direct pathway (D1 receptors, striatum→GPi→thalamus) facilitates desired movements. The indirect pathway (D2 receptors, striatum→GPe→STN→GPi→thalamus) suppresses competing movements. Dopamine from substantia nigra pars compacta (SNc) modulates this balance.

 

Cerebellum: Coordination and Motor Learning

Despite ~10% of brain volume, the cerebellum contains ~80% of all brain neurons (predominantly granule cells). Its cortex implements an internal forward model of movement, comparing intended vs. actual motor output via error signals from climbing fibers (inferior olive). This underlies motor adaptation and learning. Damage causes ataxia, dysmetria, and intention tremor.

Simulation

The interactive simulator is below. Use the controls to explore the concepts described above.

 

Usage Instructions

3D Navigation:

• Rotate — Left-click and drag on the 3D canvas to freely rotate the brain in any direction.

• Zoom — Scroll wheel to zoom in/out, or click the Z+ / Z− buttons above the canvas.

• Pan — Right-click and drag (or Ctrl + left-drag) to translate the view.

• Camera presets — Click Iso, Front, Top, Side, or Back to jump to a standard neuroimaging orientation without changing the cut-plane positions.

Region Selection:

• Click on any region in the 3D view to select it. The selected region turns solid red with a bold red halo outline and its name, category, and anatomical description appear in the Region Info panel. The same region is simultaneously highlighted in red on all three 2D cross-section views. Click empty space to deselect.

• Listbox — Browse all 37 anatomical regions grouped by category (Cerebral Cortex, Limbic System, Diencephalon, Basal Ganglia, Corpus Callosum, Brainstem, Cerebellum, Ventricular System). Click any name to highlight that region in red; the 3D camera stays where it is.

• Search — Type in the search box to filter the listbox in real time by region name or category. Press Enter to auto-select the top result.

Cut Planes (Slicing):

• X-Cut (Sagittal) — Drag the slider left to peel away the right hemisphere. At x = 0 the brain is bisected along the mid-sagittal plane, exposing the corpus callosum, thalamus, and brainstem.

• Y-Cut (Axial) — Drag the slider left to cut downward from the crown. Reveals the basal ganglia, hippocampus, and thalamus as the slice descends through the brain.

• Z-Cut (Coronal) — Drag the slider left to slice from front to back. Exposes the amygdala and deep frontal connections in an anterior coronal view.

• Combine all three sliders for compound cross-sections (e.g., X + Y produces a quadrant view showing four quadrants at once). Click Reset Cuts to restore the complete uncut brain.

2D Cross-Section Views:

• Three small 2D canvases below the 3D view update live as you move the cut-plane sliders. They show the exact anatomical cross-section at the current slider position: Sagittal (A/P × S/I at the current X value), Axial (R/L × A/P at the current Y value), and Coronal (R/L × S/I at the current Z value). Each region is drawn in its own color; the currently selected region appears in red in all three views. Orientation labels (A = Anterior, P = Posterior, S = Superior, I = Inferior, R = Right, L = Left) are shown at the canvas edges.

Layer Visibility:

• Toggle each anatomical category on/off with the checkboxes in the Layer Visibility panel. Hidden regions disappear from both the 3D view and all three 2D slice canvases simultaneously. Tip: uncheck Cerebral Cortex to reveal the subcortical and limbic structures beneath the transparent outer shell. Uncheck Ventricular System to hide the CSF-filled ventricles and reduce visual clutter when studying deep nuclei.

 

Region Color Legend

Cerebral Cortex:
■ Frontal Lobe   ■ Parietal Lobe   ■ Temporal Lobe   ■ Occipital Lobe   ■ Insula   ■ Cingulate Gyrus
Limbic System:
■ Hippocampus   ■ Amygdala
Diencephalon:
■ Thalamus   ■ Hypothalamus
Basal Ganglia:
■ Caudate   ■ Putamen   ■ Globus Pallidus   ■ Nucleus Accumbens
Corpus Callosum:
■ Genu   ■ Rostral Body   ■ Central Body   ■ Caudal Body   ■ Splenium
Brainstem:
■ Midbrain   ■ Pons   ■ Medulla   ■ Substantia Nigra
Cerebellum:
■ Cerebellar Cortex   ■ Cerebellar White Matter
Ventricular System:
■ Lateral Ventricles   ■ 3rd Ventricle   ■ 4th Ventricle

Limitations

• Schematic geometry: regions are simplified 3D shapes positioned for clarity, not a voxel-accurate reconstruction from MRI. Sizes and boundaries are approximate.
• 37 labelled regions: the model shows major structures only; the brain has hundreds of named nuclei, Brodmann areas, and white-matter tracts not represented here.
• No function/connectivity: this is a static anatomical explorer — it does not simulate neural activity, blood flow, or fiber tractography.
• Idealized symmetry: hemispheres are mirror-symmetric; real brains have normal left–right asymmetries and individual variation.