Rotate, separate, and discover the structures beneath the surface.
Offline copy & licenses
Brain Explorer with adjustable selection opacity. All model assets and code are embedded. Source links require internet. Use right drag to rotate, left drag to pan, and the scroll wheel to zoom. This copy does not include the proposed cattle-prod feature.
credits.txt
Brain Explorer model attribution
Source: https://github.com/itayinbarr/brainproject
Model and metadata redistributed unchanged. Viewer colors, grouping and exploded positions are illustrative.
## Attribution & licence
This project is **dual-licensed**. See [`LICENSE`](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.glb` model 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`](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.
BRODMANN ATLAS VIEW
Mai, J. K. & Majtanik, M. Human Brain in Standard MNI Space: A Comprehensive Pocket Atlas. Academic Press, 2017.
AFNI / NIMH distribution: https://afni.nimh.nih.gov/pub/dist/atlases/Brodmann_MM/
Coordinate metadata and label dictionary from Cedalion: https://doc.ibs.tu-berlin.de/cedalion/datasets/dev/atlas_brodmann.zip
Documentation: https://doc.ibs.tu-berlin.de/cedalion/doc/dev/examples/head_models/52_mni_atlas_labels_aal3_brodmann.html
The label voxel array was verified identical to the AFNI distribution. The Cedalion file's coordinate affine is retained.
Geometry is reconstructed from each labeled volume at 1 mm resolution, lightly smoothed (Gaussian sigma 0.55 voxels; isosurface 0.45), and simplified for interactive display. Region identity and hemisphere labels come from the source atlas. These are atlas-based surfaces, not a registration onto the gross-anatomy model and not subject-specific boundaries.
42 numbered areas are supplied per hemisphere plus an Ent region. No BA number is invented for missing atlas labels. Ent remains separate from BA34 as provided by the atlas.
assets/MODEL-LICENSE.txt
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APPENDIX: How to apply the Apache License to your work.
To apply the Apache License to your work, attach the following
boilerplate notice, with the fields enclosed by brackets "[]"
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Copyright 2026 Itay Inbar
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
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------------------------------------------------------------------------------
NOTE ON THE 3D ANATOMY ASSETS (separate licence)
The Apache 2.0 licence above covers the viewer SOURCE CODE only (HTML/CSS/JS/JSX,
build and export scripts).
The 3D geometry shipped with this project - the brain model and its derived
files, e.g. brain-atlas/models/brain.glb and the manifest/metadata derived
from it - is NOT Apache licensed. It is derived from
Z-Anatomy, which is built on BodyParts3D / DBCLS, and is licensed under
Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
https://creativecommons.org/licenses/by-sa/4.0/
If you redistribute a modified version of the model, it must remain under
CC BY-SA 4.0 and keep this attribution. See README.md ("Attribution & licence").
- Z-Anatomy - https://www.z-anatomy.com/ · https://github.com/Z-Anatomy
- BodyParts3D, © The Database Center for Life Science (DBCLS)
https://lifesciencedb.jp/bp3d/
The deep-brain nuclei (globus pallidus internal/external; the seven thalamic
nuclei groups; subthalamic nucleus, substantia nigra, nucleus accumbens; the
amygdala functional groups; the hypothalamus zones) are ADDITIONALLY derived, by
atlas-guided registration, from:
- CIT168 subcortical atlas, Pauli, Nili & Tyszka 2018, Scientific Data,
licensed CC BY 4.0 - https://osf.io/jkzwp/
- CIT168 amygdala atlas, Tyszka & Pauli 2016, licensed CC BY-SA 4.0
https://osf.io/hksa6/
- Najdenovska et al. 2018, "In-vivo probabilistic atlas of human thalamic
nuclei...", Scientific Data, licensed CC BY-SA 4.0
https://doi.org/10.5281/zenodo.1405484
- Neudorfer et al. 2020, "A high-resolution in vivo MRI atlas of the human
hypothalamic region", Scientific Data, licensed CC BY 4.0
https://doi.org/10.5281/zenodo.3942115
These derived nuclei remain under CC BY-SA 4.0 (CC BY 4.0 source material is
compatible with redistribution inside a CC BY-SA 4.0 work). They are
APPROXIMATE, registered from MNI-space atlases (~7 mm), for educational use -
not for clinical or surgical use. See docs/registration.md.
assets/THREE-LICENSE.txt
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assets/DRACO-LICENSE.txt
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