GeneLab AWG Tomography

neurology

GeneLab AWG Tomography MICRO-TOMOGRAPHY · 3D VIEWER

— LAYERS

code

K

SERIESµCT

ModalityMicro-CT SampleSample 1 Layers— SourceHugging Face ↗

ANATOMY 0

LAYERS0

linkRotation synced

Eye Anatomy

Segmented Layers

stacks

Toggle a layer to display it here.

VIEW

Anatomy & layers side by side

Show anatomy

Anatomy opacity

Anatomy X

Anatomy Y

Anatomy Z

RENDERING

Shaded surface · solid meshes

SLICE PLANESMPR

Sagittal 50%

Axial 50%

Coronal 50%

Flip cut direction Show cut planes

DISPLAY

Layer opacity 100%

X-ray view Solid fill Auto-rotate Grid floor Link sample offsets

az 0° el 0° surface 0 triangles — fps

GeneLab AWG Tomography

Two linked 3D views of GeneLab AWG retina micro-tomography: the whole eye anatomy on the left and toggleable segmented tissue layers on the right.

Controls

Rotate drag · Pan right-drag · Zoom scroll
Sync links rotation of both views
Anatomy picks which reference eye model to show, then toggles, recolours and fades each of its structures; each model brings its own presets
Rendering switches Surface / Wireframe / Slices
Slices cuts the meshes with three orthogonal planes (tri-planar MPR) to reveal interior structure

Structures tagged µCT — retina, choroid, sclera — are resolved in both panes, so the reference anatomy and the segmented scan can be read against each other.

Data

Heavy source scans are decimated and Draco-compressed, cached in your browser, and stream with a progress bar. The Hugging Face dataset is unchanged.

About

An interactive 3D viewer for segmented ocular micro-tomography — built to explore the four posterior-pole coats of the mouse eye (retina, RPE, choroid, sclera) reconstructed from NASA space-biology imaging.

Developer

Kush Shah
NASA OSDR — AI/ML Researcher
kushshah.edu@gmail.com

Data source

NASA Open Science Data Repository (OSDR), Space Biology Program, NASA Ames Research Center. F10 mouse orbital micro-computed tomography (SkyScan 1272, 4.5 µm isotropic), space-flight ocular / SANS research. osdr.nasa.gov ↗

Segmentation method

Shah, K. Unsupervised 3D segmentation of the four ocular coats from mouse orbital micro-CT (2026) — vitreous-cavity extraction, distance-transform wall detection, and radial banding by mouse posterior-pole thickness priors (retina / RPE / choroid / sclera). Meshes generated by marching cubes and hosted on Hugging Face ↗.

Reference eye models

The left pane is not NASA data — it is a published open-source eye model, shown for orientation. Pick one in the ANATOMY panel:

mesh.eye and the Feel++ CAD eye — Chabannes, V., Prud'homme, C., Saigre, T., Sala, L., Szopos, M., & Trophime, C. A 3D geometrical model and meshing procedures for the human eyeball (Cemosis, IRMA UMR 7501, Université de Strasbourg, CNRS) — feelpp/mesh.eye ↗, doi:10.5281/zenodo.13829740; described in Sala, L. et al., Int J Numer Meth Biomed Engng 2024; 40(2):e3791. GPL-3.0.

Upatras oculomotor — Stanev, D. et al. An open-source OpenSim oculomotor model for kinematics and dynamics simulation, University of Patras (arXiv:1807.07332, simtk.org/projects/eye ↗). Globe plus the six extraocular muscles, swept from the model's own path points. CC BY 4.0.

Every model is a human eye while the segmented scan is mouse; they are references for orientation, not for morphometric comparison. Structures tagged µCT are the ones resolved in both panes. Model licences are separate from this viewer's MIT code — see optimized/anatomy/README.md, which also lists the projects surveyed that ship no 3D geometry (ISETBio, OpenRetina, V-Cornea, OpenEyeSim, pulse2percept, Open Source Brain).

Acknowledgements

Rendering with Three.js (STL / glTF loaders, OrbitControls). Solid models tessellated with gmsh, decimated & Draco-compressed with glTF-Transform.