GitHub - ashemag/human-atlas: Open-source 3D anatomy explorer: 2,234 selectable BodyParts3D meshes, system layers, search, and exploded views. · GitHub

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mainBranchesTagsGo to fileCodeOpen more actions menuLatest commit History8 Commits8 CommitsFolders and filesNameNameLast commit messageLast commit dateappapp  components/uicomponents/ui  hookshooks  liblib  publicpublic  scriptsscripts  webweb  .gitignore.gitignore  LICENSELICENSE  README.mdREADME.md  package-lock.jsonpackage-lock.json  package.jsonpackage.json  tsconfig.jsontsconfig.json  vercel.jsonvercel.json  vite.config.tsvite.config.ts  View all filesRepository files navigationREADMEMIT licenseMore itemsHuman Atlas
An interactive 3D anatomy explorer built with React, Three.js, and shadcn/ui. Take the BodyParts3D adult male reference apart into 2,234 individually selectable meshes, explore 15 anatomical systems, and search 3,432 named concepts.
Explore the live demo
Explore

Orbit, zoom, and select structures directly on the body.
Toggle individual systems or use skeleton and organ presets.
Move from assembled anatomy to a spaced inventory of every visible piece.
Search anatomical names and source identifiers.
Isolate a selected structure and read its details.
Use compact controls and detail panels on mobile.

Run locally
Requires Node.js 22.13 or newer. No API keys or accounts are needed.
npm ci
npm run dev
Open http://localhost:3016. To build the static site, run npm run build; the output is in dist/.
Validate
npm run check
node scripts/validate-atlas.mjs
node scripts/validate-interactions.mjs
npm run build
Validation covers mesh buffers, names and concept membership, nonoverlapping exploded layouts at desktop and mobile aspect ratios, search and inspection contracts, and tap-versus-drag handling. Browser interaction checks have exercised selection, system controls, search, isolation, rotation, and 390×844, 320×568, and 844×390 layouts. Phone controls stay clear of the exploded inventory, and isolated structures fit the space above or beside the detail panel. Physical-device performance and real multitouch hardware have not been tested.
Anatomy data
The current viewer uses BodyParts3D 4.0, an adult male reference anatomy, licensed CC BY 4.0. It does not represent every human structure or variation. Individual source meshes are distinct from named concepts, which may group multiple meshes. Descriptions distinguish general system context from individual organ explanations.
Geometry is simplified for browser performance while retaining every source mesh. The packaged model contains 2,288,268 triangles and downloads approximately 33 MB of compressed geometry. Full credits, source links, and adaptation details are in ATTRIBUTION.md.
This is an educational explorer, not a diagnostic or surgical tool.
How it works
Geometry is merged into batches. Per-structure GPU textures control translation, visibility, and selection, while component geometry supports accurate picking. Exploded layouts pack only the visible pieces. Rendering updates when the scene changes; orbit controls remain responsive without thousands of separate draw calls.
The optional WebMCP tools expose anatomy search and inspection in compatible browsers. The visible interface works without them.
Rebuilding geometry
The repository includes browser-ready geometry. Rebuilding it is optional: obtain the official BodyParts3D OBJ archive and English metadata tables, prepare the joined concepts and display-system mappings, run scripts/convert-anatomy.py, then node scripts/optimize-anatomy.mjs and node scripts/compress-models.mjs. Simplification uses a 0.2% relative error limit per structure.
Deploy
Import this repository into Vercel as a Vite project. The included vercel.json configures npm ci, npm run build, and the dist output directory. It can also be served by a static host.
License
Original application code is released under the MIT License. The anatomy data has its own CC BY 4.0 license; preserve the attribution when redistributing it. Third-party dependencies retain their respective licenses.
Issues and pull requests are welcome. Please include reproduction steps and browser/device details for interaction problems.
AboutOpen-source 3D anatomy explorer: 2,234 selectable BodyParts3D meshes, system layers, search, and exploded views.human-atlas-seven.vercel.appResourcesReadmeMIT licenseActivityStars2.6k starsWatchers19 watchingForks666 forksReport repositoryReleasesPackagesContributorsLanguages

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The Human Atlas project is an open-source, interactive three-dimensional anatomy explorer developed as a resource for anatomical study. It provides users with access to 2,234 individually selectable BodyParts3D meshes, allowing for the exploration of 15 anatomical systems, and the capability to search across 3,432 named anatomical concepts. The core functionality enables users to orbit, zoom, and select structures directly on a 3D model, offering features such as toggling individual systems or employing skeleton and organ presets. Users can transition between an assembled anatomy view and a spaced inventory of every visible piece, facilitating detailed interaction with the anatomical data. Furthermore, the system allows for searching anatomical names and source identifiers, enabling isolation of specific structures for detailed examination of their associated information.

Technically, the explorer is built using a modern web stack, incorporating React, Three.js, and shadcn/ui for the front-end presentation. The geometry is managed through an efficient rendering process where geometry is merged into batches, and per-structure GPU textures control visibility, translation, and selection, which supports accurate picking. Exploded layouts are utilized to pack only the visible pieces of the anatomy, optimizing the view. The application is designed to handle complex spatial relationships efficiently, allowing rendering updates to occur dynamically when the scene changes while maintaining responsive orbit controls.

The anatomical data utilized in the viewer is based on BodyParts3D 4.0, which is licensed under a Creative Commons Attribution 4.0 license. The geometry has been simplified for browser performance while retaining all source meshes, resulting in a packaged model containing approximately 2,288,268 triangles and roughly 33 megabytes of compressed geometry. The project emphasizes that it functions purely as an educational tool and is not intended for diagnostic or surgical purposes.

The repository also addresses the process of geometry rebuilding. Users have the option to reconstruct the geometry by utilizing the official BodyParts3D OBJ archive and metadata tables, followed by running specific scripts to convert anatomy, optimize geometry, and compress models, adhering to a simplification limit of 0.2% relative error per structure. The project is deployed using a structure compatible with Vercel, which streamlines the process of serving the static site. While the application code itself is released under the MIT License, the underlying anatomy data carries its own CC BY 4.0 license, mandating attribution when redistributing the data. The project also includes validation scripts to ensure integrity across mesh buffers, concept membership, and user interaction contracts, demonstrating a commitment to quality assurance in data representation and browser interaction.