The most detailed interactive 3D brain available to date, free and open in your browser - and it's constantly growing.
I'm a visual learner. I've always wished for a tool that would let me actually see the brain and explore it myself, at a deeper level than just its main components. Every brain map I could find online stopped at the major regions: a dozen labelled blobs. That's not enough to truly study from. So I built the thing I wanted to exist, and I keep adding to it.
Spin it, search it, fade the cortex away, isolate a single structure, follow a white-matter tract, peel the brain apart system by system. Every gyrus and sulcus, the deep grey nuclei, the diencephalon, the white-matter pathways, the ventricles, brainstem, cerebellum, the dural venous sinuses, the circle of Willis, the dural reflections and the cranial nerves are each a separate, labelled, toggleable mesh, with its full anatomical (TA2) path and a plain-language description. This is the granularity neuroscientists and students actually need, in something anyone can open in a browser.
Nothing here is fabricated. Every mesh is a real, TA2-named anatomical structure derived from open anatomical and imaging data (full credits & licence below). The model is updated regularly as new structures are registered and refined.
- GitHub Pages: https://itayinbarr.github.io/brainproject/
- Firebase Hosting: https://brain-atlas-7f5fe.web.app
Runs entirely in the browser, no install, works on desktop and mobile (pinch-free zoom buttons on touch). Optional, consent-gated Google Analytics; declining keeps it anonymous and cookieless.
The r/neuro community gave the project a warm welcome, which has helped shape where it's headed.
No build step. The JSX is transpiled in the browser. Just serve the brain-atlas/ folder
over HTTP (the model is fetched at runtime, so opening the file directly won't work):
cd brain-atlas
python3 -m http.server 8861
# open http://localhost:8861/Three.js + React load from a CDN; the Draco decoder, the model, the data and the UI are all local. Any static host works, which is what's deployed to the live demos above.
| Action | Control |
|---|---|
| Rotate | left-drag |
| Pan / drift | hold ⌘ Cmd (or Ctrl) and left-drag, or right-drag |
| Zoom | scroll / pinch |
| Select a structure | click it in the 3D view |
| Hover | structures glow faintly under the cursor |
When you select something, its full name (with side) and its TA2 anatomical path
(e.g. Telencephalon › Frontal lobe › Precentral gyrus) appear at the bottom-left.
- Search - type any part of a name, region, or system (
calcarine,thalamus,M2,sinus,vagus,arcuate). The list filters live and non-matching meshes fade in 3D. - Layers - structures are grouped into colour-coded subsystems. Toggle a whole subsystem with its header checkbox, or expand it and toggle individual structures.
- Isolate - show only the current search matches (or the current selection), and frame the camera on them.
- Reset - restore the default view.
- Focus - fly the camera to the current selection.
- Cortex opacity - fade the cortical surface to see the deep structures, tracts, vessels and ventricles inside.
- Left / Right / Both - show one hemisphere or both (median/unpaired structures always stay visible).
- Spin (desktop) - stop or resume the idle auto-rotation.
- Share - copy a link that reopens this exact view, or download a high-definition poster.
- About - the story, credits and licence.
This is illustration-/gross-anatomy grade, derived from MRI segmentation and registered imaging atlases. Rather than chase a headline count (the number keeps changing as the model grows), here is an honest account of what is and isn't resolved, because it matters for how you use it.
- Cortex - every gyrus and sulcus, left and right, including the specific ones you'd want: calcarine sulcus, supramarginal and angular gyri, cuneus, precuneus, lingual gyrus, the fusiform (occipitotemporal) gyri, central/precentral/postcentral, parieto-occipital, etc.
- White-matter tracts - the major association, projection and commissural pathways as tube meshes (arcuate, cingulum, SLF/ILF/IFOF, uncinate, corticospinal tract, optic radiations, fornix, and more), registered from HCP1065 tract templates.
- Deep grey / basal ganglia - caudate, putamen, globus pallidus (internal/external), lentiform nucleus, amygdaloid body and its functional groups, claustrum-level structures, plus the registered subthalamic nucleus, substantia nigra and nucleus accumbens.
- Diencephalon - thalamus (whole plus the seven nuclei groups), hypothalamus and its zones, medial & lateral geniculate bodies, mamillary bodies, optic chiasm/tract, habenula, red nucleus.
- Ventricles - lateral (L/R), third, fourth, septum pellucidum, choroid plexus.
- White matter / commissures - corpus callosum, fornix, anterior & hippocampal commissures, internal capsule, stria terminalis/medullaris.
- Brainstem (midbrain/pons/medulla) with colliculi, peduncles, many cranial-nerve nuclei.
- Cerebellum with vermis/hemispheres/peduncles.
- Vasculature - the circle of Willis in full (anterior/middle/posterior cerebral arteries incl. M1/M2/M3 segments, the communicating arteries, basilar, vertebral, internal carotid, the cerebellar arteries) and the dural venous sinuses (superior/inferior sagittal, straight, transverse, sigmoid, cavernous, petrosal, confluence, etc.).
- Meninges - falx cerebri, tentorium cerebelli (the dural reflections).
- Cranial nerves I-XII and major branches, as tube meshes.
The surface-mesh structures are gross-anatomy grade. The deep nuclei, hypothalamic zones and
white-matter tracts are registered from open MNI-space imaging atlases, so they are
approximate (about 7 mm, educational, not for clinical use). The model deliberately
doesn't fake geometry it doesn't have; finer subnuclei are added only when a suitable open
atlas can be registered cleanly. See docs/registration.md for how
this is done and how to extend it.
brainmodel/
├── README.md ← this file
├── LICENSE ← Apache 2.0 (code) + CC BY-SA 4.0 (3D assets)
├── firebase.json ← Firebase Hosting config (serves brain-atlas/)
├── .github/workflows/
│ └── deploy-pages.yml ← publishes brain-atlas/ to GitHub Pages on push
├── brain-atlas/ ← the app (this is what gets deployed)
│ ├── index.html
│ ├── app.jsx ← composition, state & scene wiring
│ ├── scene.js ← Three.js scene, picking, camera, poster export
│ ├── control-panel.jsx · selection-card.jsx · layers-tree.jsx · components.jsx · …
│ ├── data.js ← structures + metadata (generated from the manifest)
│ ├── firebase-analytics.js ← consent-gated Google Analytics (Consent Mode v2)
│ ├── models/
│ │ ├── brain.glb ← Draco-compressed, every named structure
│ │ └── manifest.json ← per-structure metadata (id, label, category, side, TA2 path)
│ └── vendor/draco/ ← Draco decoder (vendored, offline-ready)
├── scripts/
│ ├── export_brain.py ← Blender: Z-Anatomy .blend → named brain.glb + manifest
│ ├── build_tracts.py ← builds white-matter tract tubes from HCP1065 centerlines
│ ├── gen_data.py ← manifest.json → data.js
│ └── shot.mjs ← headless screenshot helper (Playwright)
└── Z-Anatomy/ ← source .blend (Startup.blend) + extracted inventory
Each mesh carries its anatomy as glTF extras (so it survives Three.js name
sanitisation and Draco compression). The viewer reads these directly; it never
matches on display names:
| field | meaning |
|---|---|
bx_id |
stable unique id (one per structure; left & right are distinct) |
bx_cat |
subsystem (cortex, tracts, arteries, cranial_nerves, …) |
bx_label |
clean human label |
bx_side |
left / right / median |
bx_region |
parent region (lobe / brainstem / cerebellum …) |
manifest.json mirrors this and adds the full TA2 ancestor path per structure.
The committed brain-atlas/models/brain.glb is already built; you only need this to change
the selection, colours, or detail.
Requirements: Blender 4.x/5.x, Node 18+, and the @gltf-transform/cli + draco3dgltf
npm packages (already in this repo's node_modules).
# 1. Export the brain from the Z-Anatomy .blend → brain-atlas/models/brain.glb + manifest.json
/Applications/Blender.app/Contents/MacOS/Blender \
Z-Anatomy/Startup.blend --background --python scripts/export_brain.py
# 2. Compress for the web (dedup → weld → Draco), preserving every node + its extras
export PATH="$PWD/node_modules/.bin:$PATH"
gltf-transform dedup brain-atlas/models/brain.glb /tmp/b1.glb
gltf-transform weld /tmp/b1.glb /tmp/b2.glb
gltf-transform draco /tmp/b2.glb brain-atlas/models/brain.glbThe white-matter tracts are built separately from HCP1065 centerlines by
scripts/build_tracts.py and merged in, reusing the same affine as the registered nuclei.
- Three.js (
GLTFLoader,DRACOLoader, ACES tone mapping, a custom lightweight orbit/pan/zoom) for the 3D scene, picking and poster export. - React (+ Babel standalone) for the UI, loaded from a CDN. No bundler, no build step.
- Blender (headless Python) for the asset export; glTF-Transform for Draco compression.
This project is dual-licensed. See LICENSE for the full text:
- Viewer source code (HTML/CSS/JS/JSX, build & export scripts): Apache License 2.0. Use it, fork it, embed it, do what you like.
- 3D anatomy assets (the
brain.glbmodel and the metadata derived from it): Creative Commons Attribution-ShareAlike 4.0 (CC BY-SA 4.0), © Z-Anatomy contributors and BodyParts3D / DBCLS.
CC BY-SA is share-alike: if you distribute a modified version of the model, it must
stay under CC BY-SA and keep this attribution. The Apache 2.0 code licence does not
relicense the model; keep this notice with the .glb.
- Z-Anatomy, built on BodyParts3D, © The Database Center for Life Science (DBCLS).
Imaging-registered structures. The globus pallidus internal/external split, the thalamic
nuclei groups, the subthalamic nucleus, substantia nigra, nucleus accumbens, the amygdala
functional groups, the hypothalamus zones and the white-matter tracts are not in the source
model; they were registered from open MNI-space imaging atlases and remain CC BY-SA 4.0.
They are approximate (about 7 mm, educational, not for clinical use). How it's done and
how to extend it: docs/registration.md.
- CIT168 subcortical atlas - Pauli, Nili & Tyszka 2018, Scientific Data (CC BY 4.0) - https://osf.io/jkzwp/
- CIT168 amygdala atlas - Tyszka & Pauli 2016 (CC BY-SA 4.0) - https://osf.io/hksa6/
- Najdenovska et al. 2018, in-vivo probabilistic thalamic atlas, Scientific Data (CC BY-SA 4.0) - https://doi.org/10.5281/zenodo.1405484
- Neudorfer et al. 2020, hypothalamic region atlas, Scientific Data (CC BY 4.0) - https://doi.org/10.5281/zenodo.3942115
- HCP1065 white-matter tract templates (population-averaged, from the Human Connectome Project) used to build the tract centerlines.
Issues and PRs are welcome, especially corrections to anatomy/labels, accessibility, and new "cinematic" presets. By contributing you agree your changes are released under the same dual licence above. Please don't add fabricated geometry; this project only ships real, source-derived structures.