A 3D tool for learning where brain structures are
Knowing what a brain structure does is only half of learning neuroanatomy. The other half is knowing where it is: what sits above it, what wraps around it, and how deep it lies beneath the surface. Flat diagrams make this surprisingly hard, because a structure like the caudate nucleus curves through three dimensions and looks different in every slice. The MedMaru 3D Brain Atlas is a learning tool built for exactly this problem. It lets you rotate a model of the human brain, pick out a structure, and see its position in relation to everything around it.
Use it alongside the articles on this site. Read about a structure first, then find it in the atlas, or explore the model first and follow up with the article when a structure catches your attention.
What you can explore
The atlas groups structures the way anatomy courses usually introduce them. You can view the whole brain or select the cerebrum, the cerebellum, the basal ganglia (including the striatum, caudate nucleus, putamen, globus pallidus, subthalamic nucleus, and substantia nigra), the limbic system (including the hippocampus, fornix, mammillary bodies, amygdala, cingulate gyrus, and nucleus accumbens), the diencephalon (including the thalamus, hypothalamus, pituitary gland, and pineal gland), the brainstem (midbrain, pons, and medulla oblongata), the ventricular system, and the olfactory system.
Selecting a structure highlights it while keeping the rest of the brain visible, so you never lose your bearings. A deep-anatomy view makes the cerebral surface transparent, which is the easiest way to see how central structures such as the basal ganglia and thalamus nest inside the hemispheres.
A simple way to study with it
Start on the outside. Rotate the model and compare the positions of the four lobes and the cerebellum until you can picture them from any angle. The four lobes of the brain and the cerebellum articles explain what each region does.
Then look deeper. Switch to deep anatomy and find the basal ganglia. Notice how the striatum wraps around the thalamus, and how far down the substantia nigra sits in the midbrain. Seeing those distances in 3D makes it much easier to understand why these structures can be described as one circuit even though they are spread out.
Finally, connect what you see to what you have read. Select a structure, read its short description in the atlas, and continue to the full article for detail and references. Good places to start are what the brain is and how its main parts fit together, the diencephalon, and the brainstem.
How to use the controls
Drag to rotate the brain, pinch or scroll to zoom, and tap or click a structure to select it. Selecting the same structure again returns you to the whole-brain view. If the atlas does not load properly on your device, you can open it in a new window.
About the model
The cerebral anatomy is based on the HRA Brain (Male) reference organ, derived from the Allen Human Reference Atlas and provided through NIH 3D under a CC BY 4.0 license. The lateral ventricles use an MRI-derived model from the NIH 3D Lateral Ventricles model by Nevit Dilmen. MedMaru adapted the display, scale, orientation, and interaction. Some smaller deep structures are simplified geometry created for teaching, so their shapes are approximate.
The atlas is meant for anatomical orientation and learning. It is not a tool for diagnosis, surgical planning, measurement, or interpreting any individual’s scans.